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
289 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CGAL_HAS_BOOST_FILESYSTEM
290 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
291 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CGAL_HAS_BOOST_RANDOM
292 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CGAL_HAS_BOOST_SYSTEM
293 IMPCGAL_SHOW_WARNINGS = _IMP_em2d.IMPCGAL_SHOW_WARNINGS
295 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_em2d.IMP_ALGEBRA_HAS_IMP_CGAL
296 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
297 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
298 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_RANDOM
299 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_SYSTEM
300 IMP_ALGEBRA_HAS_CGAL = _IMP_em2d.IMP_ALGEBRA_HAS_CGAL
301 IMP_ALGEBRA_HAS_ANN = _IMP_em2d.IMP_ALGEBRA_HAS_ANN
302 IMPALGEBRA_SHOW_WARNINGS = _IMP_em2d.IMPALGEBRA_SHOW_WARNINGS
304 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_em2d.IMP_DISPLAY_HAS_IMP_CGAL
305 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
306 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
307 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_RANDOM
308 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_SYSTEM
309 IMP_DISPLAY_HAS_CGAL = _IMP_em2d.IMP_DISPLAY_HAS_CGAL
310 IMPDISPLAY_SHOW_WARNINGS = _IMP_em2d.IMPDISPLAY_SHOW_WARNINGS
312 IMP_GSL_HAS_IMP_CGAL = _IMP_em2d.IMP_GSL_HAS_IMP_CGAL
313 IMP_GSL_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_GSL_HAS_BOOST_FILESYSTEM
314 IMP_GSL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_GSL_HAS_BOOST_PROGRAMOPTIONS
315 IMP_GSL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_GSL_HAS_BOOST_RANDOM
316 IMP_GSL_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_GSL_HAS_BOOST_SYSTEM
317 IMP_GSL_HAS_CGAL = _IMP_em2d.IMP_GSL_HAS_CGAL
318 IMPGSL_SHOW_WARNINGS = _IMP_em2d.IMPGSL_SHOW_WARNINGS
320 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
321 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
322 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
323 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
324 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
325 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_CGAL
326 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_HDF5
327 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_em2d.IMPSCOREFUNCTOR_SHOW_WARNINGS
329 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_em2d.IMP_STATISTICS_HAS_IMP_CGAL
330 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
331 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
332 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_RANDOM
333 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_SYSTEM
334 IMP_STATISTICS_HAS_CGAL = _IMP_em2d.IMP_STATISTICS_HAS_CGAL
335 IMPSTATISTICS_SHOW_WARNINGS = _IMP_em2d.IMPSTATISTICS_SHOW_WARNINGS
337 IMP_CORE_HAS_IMP_CGAL = _IMP_em2d.IMP_CORE_HAS_IMP_CGAL
338 IMP_CORE_HAS_IMP_KERNEL = _IMP_em2d.IMP_CORE_HAS_IMP_KERNEL
339 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CORE_HAS_BOOST_FILESYSTEM
340 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
341 IMP_CORE_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CORE_HAS_BOOST_RANDOM
342 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CORE_HAS_BOOST_SYSTEM
343 IMP_CORE_HAS_CGAL = _IMP_em2d.IMP_CORE_HAS_CGAL
344 IMP_CORE_HAS_HDF5 = _IMP_em2d.IMP_CORE_HAS_HDF5
345 IMPCORE_SHOW_WARNINGS = _IMP_em2d.IMPCORE_SHOW_WARNINGS
347 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_em2d.IMP_CONTAINER_HAS_IMP_ALGEBRA
348 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_em2d.IMP_CONTAINER_HAS_IMP_CGAL
349 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_em2d.IMP_CONTAINER_HAS_IMP_DISPLAY
350 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_em2d.IMP_CONTAINER_HAS_IMP_KERNEL
351 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
352 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
353 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
354 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_RANDOM
355 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_SYSTEM
356 IMP_CONTAINER_HAS_CGAL = _IMP_em2d.IMP_CONTAINER_HAS_CGAL
357 IMP_CONTAINER_HAS_HDF5 = _IMP_em2d.IMP_CONTAINER_HAS_HDF5
358 IMPCONTAINER_SHOW_WARNINGS = _IMP_em2d.IMPCONTAINER_SHOW_WARNINGS
360 IMP_ATOM_HAS_IMP_CGAL = _IMP_em2d.IMP_ATOM_HAS_IMP_CGAL
361 IMP_ATOM_HAS_IMP_KERNEL = _IMP_em2d.IMP_ATOM_HAS_IMP_KERNEL
362 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
363 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
364 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_em2d.IMP_ATOM_HAS_BOOST_RANDOM
365 IMP_ATOM_HAS_BOOST_REGEX = _IMP_em2d.IMP_ATOM_HAS_BOOST_REGEX
366 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_ATOM_HAS_BOOST_SYSTEM
367 IMP_ATOM_HAS_CGAL = _IMP_em2d.IMP_ATOM_HAS_CGAL
368 IMP_ATOM_HAS_HDF5 = _IMP_em2d.IMP_ATOM_HAS_HDF5
369 IMPATOM_SHOW_WARNINGS = _IMP_em2d.IMPATOM_SHOW_WARNINGS
370 IMP_ATOM_TYPE_INDEX = _IMP_em2d.IMP_ATOM_TYPE_INDEX
371 IMP_RESIDUE_TYPE_INDEX = _IMP_em2d.IMP_RESIDUE_TYPE_INDEX
372 IMP_HIERARCHY_TYPE_INDEX = _IMP_em2d.IMP_HIERARCHY_TYPE_INDEX
374 IMP_EM_HAS_IMP_CGAL = _IMP_em2d.IMP_EM_HAS_IMP_CGAL
375 IMP_EM_HAS_IMP_CONTAINER = _IMP_em2d.IMP_EM_HAS_IMP_CONTAINER
376 IMP_EM_HAS_IMP_DISPLAY = _IMP_em2d.IMP_EM_HAS_IMP_DISPLAY
377 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_EM_HAS_IMP_SCORE_FUNCTOR
378 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_EM_HAS_BOOST_FILESYSTEM
379 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
380 IMP_EM_HAS_BOOST_RANDOM = _IMP_em2d.IMP_EM_HAS_BOOST_RANDOM
381 IMP_EM_HAS_BOOST_REGEX = _IMP_em2d.IMP_EM_HAS_BOOST_REGEX
382 IMP_EM_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_EM_HAS_BOOST_SYSTEM
383 IMP_EM_HAS_CGAL = _IMP_em2d.IMP_EM_HAS_CGAL
384 IMP_EM_HAS_HDF5 = _IMP_em2d.IMP_EM_HAS_HDF5
385 IMPEM_SHOW_WARNINGS = _IMP_em2d.IMPEM_SHOW_WARNINGS
387 IMP_RMF_HAS_IMP_CGAL = _IMP_em2d.IMP_RMF_HAS_IMP_CGAL
388 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
389 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_RMF_HAS_BOOST_FILESYSTEM
390 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
391 IMP_RMF_HAS_BOOST_RANDOM = _IMP_em2d.IMP_RMF_HAS_BOOST_RANDOM
392 IMP_RMF_HAS_BOOST_REGEX = _IMP_em2d.IMP_RMF_HAS_BOOST_REGEX
393 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_RMF_HAS_BOOST_SYSTEM
394 IMP_RMF_HAS_CGAL = _IMP_em2d.IMP_RMF_HAS_CGAL
395 IMP_RMF_HAS_HDF5 = _IMP_em2d.IMP_RMF_HAS_HDF5
396 IMPRMF_SHOW_WARNINGS = _IMP_em2d.IMPRMF_SHOW_WARNINGS
399 IMP_DOMINO_HAS_IMP_ATOM = _IMP_em2d.IMP_DOMINO_HAS_IMP_ATOM
400 IMP_DOMINO_HAS_IMP_CGAL = _IMP_em2d.IMP_DOMINO_HAS_IMP_CGAL
401 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_em2d.IMP_DOMINO_HAS_IMP_KERNEL
402 IMP_DOMINO_HAS_IMP_RMF = _IMP_em2d.IMP_DOMINO_HAS_IMP_RMF
403 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
404 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_FILESYSTEM
405 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
406 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_RANDOM
407 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_em2d.IMP_DOMINO_HAS_BOOST_REGEX
408 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_SYSTEM
409 IMP_DOMINO_HAS_CGAL = _IMP_em2d.IMP_DOMINO_HAS_CGAL
410 IMP_DOMINO_HAS_HDF5 = _IMP_em2d.IMP_DOMINO_HAS_HDF5
411 IMP_DOMINO_HAS_RMF = _IMP_em2d.IMP_DOMINO_HAS_RMF
412 IMPDOMINO_SHOW_WARNINGS = _IMP_em2d.IMPDOMINO_SHOW_WARNINGS
415 IMP_EM2D_HAS_IMP_CGAL = _IMP_em2d.IMP_EM2D_HAS_IMP_CGAL
416 IMP_EM2D_HAS_IMP_KERNEL = _IMP_em2d.IMP_EM2D_HAS_IMP_KERNEL
417 IMP_EM2D_HAS_IMP_RMF = _IMP_em2d.IMP_EM2D_HAS_IMP_RMF
418 IMP_EM2D_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_EM2D_HAS_IMP_SCORE_FUNCTOR
419 IMP_EM2D_HAS_IMP_STATISTICS = _IMP_em2d.IMP_EM2D_HAS_IMP_STATISTICS
420 IMP_EM2D_HAS_BOOST_GRAPH = _IMP_em2d.IMP_EM2D_HAS_BOOST_GRAPH
421 IMP_EM2D_HAS_BOOST_RANDOM = _IMP_em2d.IMP_EM2D_HAS_BOOST_RANDOM
422 IMP_EM2D_HAS_BOOST_REGEX = _IMP_em2d.IMP_EM2D_HAS_BOOST_REGEX
423 IMP_EM2D_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_EM2D_HAS_BOOST_SYSTEM
424 IMP_EM2D_HAS_CGAL = _IMP_em2d.IMP_EM2D_HAS_CGAL
425 IMP_EM2D_HAS_GSL = _IMP_em2d.IMP_EM2D_HAS_GSL
426 IMP_EM2D_HAS_HDF5 = _IMP_em2d.IMP_EM2D_HAS_HDF5
427 IMP_EM2D_HAS_OPENCV22 = _IMP_em2d.IMP_EM2D_HAS_OPENCV22
428 IMP_EM2D_HAS_RMF = _IMP_em2d.IMP_EM2D_HAS_RMF
429 IMP_EM2D_HAS_OPENCV21 = _IMP_em2d.IMP_EM2D_HAS_OPENCV21
430 IMP_EM2D_HAS_OPENCV3 = _IMP_em2d.IMP_EM2D_HAS_OPENCV3
431 IMPEM2D_SHOW_WARNINGS = _IMP_em2d.IMPEM2D_SHOW_WARNINGS
433 PolarResamplingParametersList=list
434 _plural_types.append(
"PolarResamplingParametersList")
435 _value_types.append(
"PolarResamplingParameters")
439 _plural_types.append(
"ProjectionMasks")
440 _value_types.append(
"ProjectionMask")
444 _plural_types.append(
"MasksManagers")
445 _value_types.append(
"MasksManager")
448 RegistrationResults=list
449 _plural_types.append(
"RegistrationResults")
450 _value_types.append(
"RegistrationResult")
454 _plural_types.append(
"ClusterSets")
455 _value_types.append(
"ClusterSet")
459 _plural_types.append(
"SingleLinkages")
460 _value_types.append(
"SingleLinkage")
463 CompleteLinkages=list
464 _plural_types.append(
"CompleteLinkages")
465 _value_types.append(
"CompleteLinkage")
468 AverageDistanceLinkages=list
469 _plural_types.append(
"AverageDistanceLinkages")
470 _value_types.append(
"AverageDistanceLinkage")
473 SegmentationParametersList=list
474 _plural_types.append(
"SegmentationParametersList")
475 _value_types.append(
"SegmentationParameters")
478 MatchTemplateResults=list
479 _plural_types.append(
"MatchTemplateResults")
480 _value_types.append(
"MatchTemplateResult")
483 ProjectingParametersList=list
484 _plural_types.append(
"ProjectingParametersList")
485 _value_types.append(
"ProjectingParameters")
488 ProjectingOptionsList=list
489 _plural_types.append(
"ProjectingOptionsList")
490 _value_types.append(
"ProjectingOptions")
493 Em2DRestraintParametersList=list
494 _plural_types.append(
"Em2DRestraintParametersList")
495 _value_types.append(
"Em2DRestraintParameters")
498 _object_types.append(
"ProjectionFinder")
501 def _object_cast_to_ProjectionFinder(o):
502 """_object_cast_to_ProjectionFinder(Object o) -> ProjectionFinder"""
503 return _IMP_em2d._object_cast_to_ProjectionFinder(o)
505 _object_types.append(
"ScoreFunction")
508 def _object_cast_to_ScoreFunction(o):
509 """_object_cast_to_ScoreFunction(Object o) -> ScoreFunction"""
510 return _IMP_em2d._object_cast_to_ScoreFunction(o)
512 _object_types.append(
"ChiSquaredScore")
515 def _object_cast_to_ChiSquaredScore(o):
516 """_object_cast_to_ChiSquaredScore(Object o) -> ChiSquaredScore"""
517 return _IMP_em2d._object_cast_to_ChiSquaredScore(o)
519 _object_types.append(
"EM2DScore")
522 def _object_cast_to_EM2DScore(o):
523 """_object_cast_to_EM2DScore(Object o) -> EM2DScore"""
524 return _IMP_em2d._object_cast_to_EM2DScore(o)
526 _object_types.append(
"MeanAbsoluteDifference")
529 def _object_cast_to_MeanAbsoluteDifference(o):
530 """_object_cast_to_MeanAbsoluteDifference(Object o) -> MeanAbsoluteDifference"""
531 return _IMP_em2d._object_cast_to_MeanAbsoluteDifference(o)
533 _object_types.append(
"ProjectionParametersScoreState")
536 def _object_cast_to_ProjectionParametersScoreState(o):
537 """_object_cast_to_ProjectionParametersScoreState(Object o) -> ProjectionParametersScoreState"""
538 return _IMP_em2d._object_cast_to_ProjectionParametersScoreState(o)
540 _object_types.append(
"Em2DRestraint")
543 def _object_cast_to_Em2DRestraint(o):
544 """_object_cast_to_Em2DRestraint(Object o) -> Em2DRestraint"""
545 return _IMP_em2d._object_cast_to_Em2DRestraint(o)
547 _object_types.append(
"Image")
550 def _object_cast_to_Image(o):
551 """_object_cast_to_Image(Object o) -> Image"""
552 return _IMP_em2d._object_cast_to_Image(o)
554 _object_types.append(
"ImageReaderWriter")
557 def _object_cast_to_ImageReaderWriter(o):
558 """_object_cast_to_ImageReaderWriter(Object o) -> ImageReaderWriter"""
559 return _IMP_em2d._object_cast_to_ImageReaderWriter(o)
561 _object_types.append(
"JPGImageReaderWriter")
564 def _object_cast_to_JPGImageReaderWriter(o):
565 """_object_cast_to_JPGImageReaderWriter(Object o) -> JPGImageReaderWriter"""
566 return _IMP_em2d._object_cast_to_JPGImageReaderWriter(o)
568 _object_types.append(
"TIFFImageReaderWriter")
571 def _object_cast_to_TIFFImageReaderWriter(o):
572 """_object_cast_to_TIFFImageReaderWriter(Object o) -> TIFFImageReaderWriter"""
573 return _IMP_em2d._object_cast_to_TIFFImageReaderWriter(o)
575 _object_types.append(
"SpiderImageReaderWriter")
578 def _object_cast_to_SpiderImageReaderWriter(o):
579 """_object_cast_to_SpiderImageReaderWriter(Object o) -> SpiderImageReaderWriter"""
580 return _IMP_em2d._object_cast_to_SpiderImageReaderWriter(o)
582 _object_types.append(
"CollisionCrossSection")
585 def _object_cast_to_CollisionCrossSection(o):
586 """_object_cast_to_CollisionCrossSection(Object o) -> CollisionCrossSection"""
587 return _IMP_em2d._object_cast_to_CollisionCrossSection(o)
589 _object_types.append(
"GridStates")
592 def _object_cast_to_GridStates(o):
593 """_object_cast_to_GridStates(Object o) -> GridStates"""
594 return _IMP_em2d._object_cast_to_GridStates(o)
596 _object_types.append(
"ProjectionStates")
599 def _object_cast_to_ProjectionStates(o):
600 """_object_cast_to_ProjectionStates(Object o) -> ProjectionStates"""
601 return _IMP_em2d._object_cast_to_ProjectionStates(o)
603 _object_types.append(
"DistanceFilter")
606 def _object_cast_to_DistanceFilter(o):
607 """_object_cast_to_DistanceFilter(Object o) -> DistanceFilter"""
608 return _IMP_em2d._object_cast_to_DistanceFilter(o)
610 _object_types.append(
"DistanceFilterTable")
613 def _object_cast_to_DistanceFilterTable(o):
614 """_object_cast_to_DistanceFilterTable(Object o) -> DistanceFilterTable"""
615 return _IMP_em2d._object_cast_to_DistanceFilterTable(o)
617 _object_types.append(
"RigidBodiesImageFitRestraint")
620 def _object_cast_to_RigidBodiesImageFitRestraint(o):
621 """_object_cast_to_RigidBodiesImageFitRestraint(Object o) -> RigidBodiesImageFitRestraint"""
622 return _IMP_em2d._object_cast_to_RigidBodiesImageFitRestraint(o)
624 _object_types.append(
"DummyRestraint")
627 def _object_cast_to_DummyRestraint(o):
628 """_object_cast_to_DummyRestraint(Object o) -> DummyRestraint"""
629 return _IMP_em2d._object_cast_to_DummyRestraint(o)
631 _object_types.append(
"ParticlesDummyRestraint")
634 def _object_cast_to_ParticlesDummyRestraint(o):
635 """_object_cast_to_ParticlesDummyRestraint(Object o) -> ParticlesDummyRestraint"""
636 return _IMP_em2d._object_cast_to_ParticlesDummyRestraint(o)
638 _object_types.append(
"RelativePositionMover")
641 def _object_cast_to_RelativePositionMover(o):
642 """_object_cast_to_RelativePositionMover(Object o) -> RelativePositionMover"""
643 return _IMP_em2d._object_cast_to_RelativePositionMover(o)
645 _object_types.append(
"PCAFitRestraint")
648 def _object_cast_to_em2dPCAFitRestraint(o):
649 """_object_cast_to_em2dPCAFitRestraint(Object o) -> PCAFitRestraint"""
650 return _IMP_em2d._object_cast_to_em2dPCAFitRestraint(o)
652 def ProjectionParametersList(l=[]):
653 return [ProjectionParameters(x)
for x
in l]
654 _plural_types.append(
"ProjectionParametersList")
657 _value_types.append(
"ProjectionParameters")
662 show(cv::Mat const & m, _ostream out)
663 show(cv::Mat const & m)
665 return _IMP_em2d.show(*args)
668 """write_matrix(cv::Mat & m, std::string name)"""
669 return _IMP_em2d.write_matrix(m, name)
671 """Proxy of C++ IMP::em2d::ImageReaderWriter class."""
673 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
675 def __init__(self, *args, **kwargs):
676 raise AttributeError(
"No constructor defined - class is abstract")
678 def read(self, filename, header, data):
679 """read(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
680 return _IMP_em2d.ImageReaderWriter_read(self, filename, header, data)
683 def read_from_floats(self, filename, header, data):
684 """read_from_floats(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
685 return _IMP_em2d.ImageReaderWriter_read_from_floats(self, filename, header, data)
688 def read_from_ints(self, filename, header, data):
689 """read_from_ints(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
690 return _IMP_em2d.ImageReaderWriter_read_from_ints(self, filename, header, data)
693 def write(self, filename, header, data):
694 """write(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
695 return _IMP_em2d.ImageReaderWriter_write(self, filename, header, data)
698 def write_to_floats(self, filename, header, data):
699 """write_to_floats(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
700 return _IMP_em2d.ImageReaderWriter_write_to_floats(self, filename, header, data)
703 def write_to_ints(self, filename, header, data):
704 """write_to_ints(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
705 return _IMP_em2d.ImageReaderWriter_write_to_ints(self, filename, header, data)
708 def get_version_info(self):
709 """get_version_info(ImageReaderWriter self) -> VersionInfo"""
710 return _IMP_em2d.ImageReaderWriter_get_version_info(self)
714 """__str__(ImageReaderWriter self) -> std::string"""
715 return _IMP_em2d.ImageReaderWriter___str__(self)
719 """__repr__(ImageReaderWriter self) -> std::string"""
720 return _IMP_em2d.ImageReaderWriter___repr__(self)
725 return _object_cast_to_ImageReaderWriter(o)
727 ImageReaderWriter_swigregister = _IMP_em2d.ImageReaderWriter_swigregister
728 ImageReaderWriter_swigregister(ImageReaderWriter)
730 class PolarResamplingParameters(object):
731 """Proxy of C++ IMP::em2d::PolarResamplingParameters class."""
733 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
735 def __init__(self, *args):
737 __init__(IMP::em2d::PolarResamplingParameters self) -> PolarResamplingParameters
738 __init__(IMP::em2d::PolarResamplingParameters self, unsigned int rows, unsigned int cols) -> PolarResamplingParameters
739 __init__(IMP::em2d::PolarResamplingParameters self, cv::Mat const & m) -> PolarResamplingParameters
741 this = _IMP_em2d.new_PolarResamplingParameters(*args)
743 self.this.append(this)
744 except __builtin__.Exception:
746 __swig_destroy__ = _IMP_em2d.delete_PolarResamplingParameters
747 __del__ =
lambda self:
None
749 def setup(self, rows, cols):
750 """setup(PolarResamplingParameters self, unsigned int rows, unsigned int cols)"""
751 return _IMP_em2d.PolarResamplingParameters_setup(self, rows, cols)
754 def get_starting_radius(self):
755 """get_starting_radius(PolarResamplingParameters self) -> double"""
756 return _IMP_em2d.PolarResamplingParameters_get_starting_radius(self)
759 def get_ending_radius(self):
760 """get_ending_radius(PolarResamplingParameters self) -> double"""
761 return _IMP_em2d.PolarResamplingParameters_get_ending_radius(self)
764 def get_radius(self, n_ring):
765 """get_radius(PolarResamplingParameters self, unsigned int n_ring) -> double"""
766 return _IMP_em2d.PolarResamplingParameters_get_radius(self, n_ring)
769 def get_number_of_rings(self):
770 """get_number_of_rings(PolarResamplingParameters self) -> unsigned int"""
771 return _IMP_em2d.PolarResamplingParameters_get_number_of_rings(self)
774 def set_estimated_number_of_angles(self, aprox_value):
775 """set_estimated_number_of_angles(PolarResamplingParameters self, unsigned int aprox_value)"""
776 return _IMP_em2d.PolarResamplingParameters_set_estimated_number_of_angles(self, aprox_value)
779 def get_number_of_angles(self):
780 """get_number_of_angles(PolarResamplingParameters self) -> unsigned int"""
781 return _IMP_em2d.PolarResamplingParameters_get_number_of_angles(self)
784 def get_angle_step(self):
785 """get_angle_step(PolarResamplingParameters self) -> double"""
786 return _IMP_em2d.PolarResamplingParameters_get_angle_step(self)
789 def get_radius_step(self):
790 """get_radius_step(PolarResamplingParameters self) -> double"""
791 return _IMP_em2d.PolarResamplingParameters_get_radius_step(self)
794 def create_maps_for_resampling(self):
795 """create_maps_for_resampling(PolarResamplingParameters self)"""
796 return _IMP_em2d.PolarResamplingParameters_create_maps_for_resampling(self)
799 def get_resampling_maps(self, m1, m2):
800 """get_resampling_maps(PolarResamplingParameters self, cv::Mat & m1, cv::Mat & m2)"""
801 return _IMP_em2d.PolarResamplingParameters_get_resampling_maps(self, m1, m2)
804 def get_resampling_map(self, m1):
805 """get_resampling_map(PolarResamplingParameters self, cv::Mat & m1)"""
806 return _IMP_em2d.PolarResamplingParameters_get_resampling_map(self, m1)
810 """show(PolarResamplingParameters self, _ostream out)"""
811 return _IMP_em2d.PolarResamplingParameters_show(self, out)
814 def get_is_setup(self):
815 """get_is_setup(PolarResamplingParameters self) -> bool"""
816 return _IMP_em2d.PolarResamplingParameters_get_is_setup(self)
820 """__str__(PolarResamplingParameters self) -> std::string"""
821 return _IMP_em2d.PolarResamplingParameters___str__(self)
825 """__repr__(PolarResamplingParameters self) -> std::string"""
826 return _IMP_em2d.PolarResamplingParameters___repr__(self)
828 PolarResamplingParameters_swigregister = _IMP_em2d.PolarResamplingParameters_swigregister
829 PolarResamplingParameters_swigregister(PolarResamplingParameters)
831 class SegmentationParameters(object):
832 """Proxy of C++ IMP::em2d::SegmentationParameters class."""
834 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
835 image_pixel_size = _swig_property(_IMP_em2d.SegmentationParameters_image_pixel_size_get, _IMP_em2d.SegmentationParameters_image_pixel_size_set)
836 diffusion_beta = _swig_property(_IMP_em2d.SegmentationParameters_diffusion_beta_get, _IMP_em2d.SegmentationParameters_diffusion_beta_set)
837 diffusion_timesteps = _swig_property(_IMP_em2d.SegmentationParameters_diffusion_timesteps_get, _IMP_em2d.SegmentationParameters_diffusion_timesteps_set)
838 fill_holes_stddevs = _swig_property(_IMP_em2d.SegmentationParameters_fill_holes_stddevs_get, _IMP_em2d.SegmentationParameters_fill_holes_stddevs_set)
839 opening_kernel = _swig_property(_IMP_em2d.SegmentationParameters_opening_kernel_get, _IMP_em2d.SegmentationParameters_opening_kernel_set)
840 remove_sizing_percentage = _swig_property(_IMP_em2d.SegmentationParameters_remove_sizing_percentage_get, _IMP_em2d.SegmentationParameters_remove_sizing_percentage_set)
841 binary_background = _swig_property(_IMP_em2d.SegmentationParameters_binary_background_get, _IMP_em2d.SegmentationParameters_binary_background_set)
842 binary_foreground = _swig_property(_IMP_em2d.SegmentationParameters_binary_foreground_get, _IMP_em2d.SegmentationParameters_binary_foreground_set)
843 threshold = _swig_property(_IMP_em2d.SegmentationParameters_threshold_get, _IMP_em2d.SegmentationParameters_threshold_set)
845 def __init__(self, *args):
847 __init__(IMP::em2d::SegmentationParameters self) -> SegmentationParameters
848 __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
850 this = _IMP_em2d.new_SegmentationParameters(*args)
852 self.this.append(this)
853 except __builtin__.Exception:
856 def show(self, *args):
858 show(SegmentationParameters self, _ostream out)
859 show(SegmentationParameters self)
861 return _IMP_em2d.SegmentationParameters_show(self, *args)
865 """__str__(SegmentationParameters self) -> std::string"""
866 return _IMP_em2d.SegmentationParameters___str__(self)
870 """__repr__(SegmentationParameters self) -> std::string"""
871 return _IMP_em2d.SegmentationParameters___repr__(self)
873 __swig_destroy__ = _IMP_em2d.delete_SegmentationParameters
874 __del__ =
lambda self:
None
875 SegmentationParameters_swigregister = _IMP_em2d.SegmentationParameters_swigregister
876 SegmentationParameters_swigregister(SegmentationParameters)
878 class MatchTemplateResult(object):
879 """Proxy of C++ IMP::em2d::MatchTemplateResult class."""
881 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
882 pair = _swig_property(_IMP_em2d.MatchTemplateResult_pair_get, _IMP_em2d.MatchTemplateResult_pair_set)
883 cross_correlation = _swig_property(_IMP_em2d.MatchTemplateResult_cross_correlation_get, _IMP_em2d.MatchTemplateResult_cross_correlation_set)
885 def __init__(self, p, cc):
886 """__init__(IMP::em2d::MatchTemplateResult self, IMP::IntPair p, double cc) -> MatchTemplateResult"""
887 this = _IMP_em2d.new_MatchTemplateResult(p, cc)
889 self.this.append(this)
890 except __builtin__.Exception:
893 def show(self, *args):
895 show(MatchTemplateResult self, _ostream out)
896 show(MatchTemplateResult self)
898 return _IMP_em2d.MatchTemplateResult_show(self, *args)
902 """__str__(MatchTemplateResult self) -> std::string"""
903 return _IMP_em2d.MatchTemplateResult___str__(self)
907 """__repr__(MatchTemplateResult self) -> std::string"""
908 return _IMP_em2d.MatchTemplateResult___repr__(self)
910 __swig_destroy__ = _IMP_em2d.delete_MatchTemplateResult
911 __del__ =
lambda self:
None
912 MatchTemplateResult_swigregister = _IMP_em2d.MatchTemplateResult_swigregister
913 MatchTemplateResult_swigregister(MatchTemplateResult)
917 """apply_mask(cv::Mat const & m, cv::Mat & result, IMP::em2d::cvIntMat const & mask, double val)"""
918 return _IMP_em2d.apply_mask(m, result, mask, val)
922 apply_circular_mask(cv::Mat const & mat, cv::Mat & result, int radius, double value=0.0)
923 apply_circular_mask(cv::Mat const & mat, cv::Mat & result, int radius)
925 return _IMP_em2d.apply_circular_mask(mat, result, radius, value)
928 """get_mean(cv::Mat const & mat, IMP::em2d::cvIntMat const & mask) -> double"""
929 return _IMP_em2d.get_mean(mat, mask)
932 """create_circular_mask(int rows, int cols, int radius) -> IMP::em2d::cvIntMat"""
933 return _IMP_em2d.create_circular_mask(rows, cols, radius)
935 def do_histogram_stretching(m, boxes, offset):
936 """do_histogram_stretching(cv::Mat & m, int boxes, int offset)"""
937 return _IMP_em2d.do_histogram_stretching(m, boxes, offset)
940 """do_dilate_and_shrink_warp(cv::Mat & m, cv::Mat const & grayscale, cv::Mat & kernel)"""
941 return _IMP_em2d.do_dilate_and_shrink_warp(m, grayscale, kernel)
945 do_morphologic_reconstruction(cv::Mat const & mask, cv::Mat & marker, int neighbors_mode=4)
946 do_morphologic_reconstruction(cv::Mat const & mask, cv::Mat & marker)
948 return _IMP_em2d.do_morphologic_reconstruction(mask, marker, neighbors_mode)
951 """do_labeling(IMP::em2d::cvIntMat const & m, IMP::em2d::cvIntMat & mat_to_label) -> int"""
952 return _IMP_em2d.do_labeling(m, mat_to_label)
955 """get_diffusion_filtering_partial_derivative(cv::Mat const & m, cv::Mat & der, double dx, double dy, double ang)"""
956 return _IMP_em2d.get_diffusion_filtering_partial_derivative(m, der, dx, dy, ang)
959 """get_domes(cv::Mat & m, cv::Mat & result, double h)"""
960 return _IMP_em2d.get_domes(m, result, h)
962 def get_transformed(input, transformed, T):
963 """get_transformed(cv::Mat const & input, cv::Mat & transformed, Transformation2D T)"""
964 return _IMP_em2d.get_transformed(input, transformed, T)
968 apply_threshold(cv::Mat & m, cv::Mat & result, double threshold=0.0)
969 apply_threshold(cv::Mat & m, cv::Mat & result)
971 return _IMP_em2d.apply_threshold(m, result, threshold)
974 """do_morphologic_contrast_enhancement(cv::Mat const & m, cv::Mat & result, cv::Mat const & kernel, unsigned int iterations)"""
975 return _IMP_em2d.do_morphologic_contrast_enhancement(m, result, kernel, iterations)
978 """get_morphologic_gradient(cv::Mat const & m, cv::Mat & result, cv::Mat const & kernel)"""
979 return _IMP_em2d.get_morphologic_gradient(m, result, kernel)
982 """get_overlap_percentage(cv::Mat & m1, cv::Mat & m2, IMP::IntPair const & center) -> double"""
983 return _IMP_em2d.get_overlap_percentage(m1, m2, center)
986 """get_best_template_matches(cv::Mat const & m, cv::Mat const & templ, unsigned int n) -> IMP::em2d::MatchTemplateResults"""
987 return _IMP_em2d.get_best_template_matches(m, templ, n)
989 """Proxy of C++ IMP::em2d::Image class."""
991 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
993 def __init__(self, *args):
995 __init__(IMP::em2d::Image self) -> Image
996 __init__(IMP::em2d::Image self, int rows, int cols) -> Image
997 __init__(IMP::em2d::Image self, IMP::String filename, ImageReaderWriter reader) -> Image
999 this = _IMP_em2d.new_Image(*args)
1001 self.this.append(this)
1002 except __builtin__.Exception:
1006 """get_data(Image self) -> cv::Mat &"""
1007 return _IMP_em2d.Image_get_data(self)
1010 def set_data(self, mat):
1011 """set_data(Image self, cv::Mat const & mat)"""
1012 return _IMP_em2d.Image_set_data(self, mat)
1015 def set_zeros(self):
1016 """set_zeros(Image self)"""
1017 return _IMP_em2d.Image_set_zeros(self)
1020 def set_value(self, *args):
1022 set_value(Image self, double val)
1023 set_value(Image self, int i, int j, double val)
1025 return _IMP_em2d.Image_set_value(self, *args)
1028 def __call__(self, i, j):
1029 """__call__(Image self, int i, int j) -> double"""
1030 return _IMP_em2d.Image___call__(self, i, j)
1033 def get_header(self):
1034 """get_header(Image self) -> ImageHeader"""
1035 return _IMP_em2d.Image_get_header(self)
1038 def set_size(self, *args):
1040 set_size(Image self, int rows, int cols)
1041 set_size(Image self, Image img)
1043 return _IMP_em2d.Image_set_size(self, *args)
1046 def update_header(self):
1047 """update_header(Image self)"""
1048 return _IMP_em2d.Image_update_header(self)
1051 def read(self, filename, reader):
1052 """read(Image self, IMP::String filename, ImageReaderWriter reader)"""
1053 return _IMP_em2d.Image_read(self, filename, reader)
1056 def write(self, filename, writer):
1057 """write(Image self, IMP::String const & filename, ImageReaderWriter writer)"""
1058 return _IMP_em2d.Image_write(self, filename, writer)
1061 def show(self, out):
1062 """show(Image self, _ostream out)"""
1063 return _IMP_em2d.Image_show(self, out)
1066 def get_version_info(self):
1067 """get_version_info(Image self) -> VersionInfo"""
1068 return _IMP_em2d.Image_get_version_info(self)
1071 def set_name(self, name):
1072 """set_name(Image self, IMP::String const & name)"""
1073 return _IMP_em2d.Image_set_name(self, name)
1077 """get_name(Image self) -> IMP::String"""
1078 return _IMP_em2d.Image_get_name(self)
1081 def get_min_and_max_values(self):
1082 """get_min_and_max_values(Image self) -> IMP::FloatRange"""
1083 return _IMP_em2d.Image_get_min_and_max_values(self)
1087 """__str__(Image self) -> std::string"""
1088 return _IMP_em2d.Image___str__(self)
1092 """__repr__(Image self) -> std::string"""
1093 return _IMP_em2d.Image___repr__(self)
1098 return _object_cast_to_Image(o)
1100 Image_swigregister = _IMP_em2d.Image_swigregister
1101 Image_swigregister(Image)
1105 """read_images(IMP::Strings const & names, ImageReaderWriter rw) -> IMP::em2d::Images"""
1106 return _IMP_em2d.read_images(names, rw)
1109 """save_images(IMP::em2d::Images images, IMP::Strings const & names, ImageReaderWriter rw)"""
1110 return _IMP_em2d.save_images(images, names, rw)
1114 do_normalize(cv::Mat & m)
1115 do_normalize(Image im, bool force=False)
1116 do_normalize(Image im)
1118 return _IMP_em2d.do_normalize(*args)
1122 get_histogram(cv::Mat const & m, int bins) -> IMP::Floats
1123 get_histogram(Image img, int bins) -> IMP::Floats
1125 return _IMP_em2d.get_histogram(*args)
1129 apply_variance_filter(cv::Mat const & input, cv::Mat & filtered, int kernelsize)
1130 apply_variance_filter(Image input, Image filtered, int kernelsize)
1132 return _IMP_em2d.apply_variance_filter(*args)
1136 apply_diffusion_filter(cv::Mat const & m, cv::Mat & result, double beta, double pixelsize, unsigned int time_steps)
1137 apply_diffusion_filter(Image input, Image filtered, double beta, double pixelsize, int time_steps)
1139 return _IMP_em2d.apply_diffusion_filter(*args)
1141 def do_fill_holes(*args):
1143 do_fill_holes(cv::Mat const & m, cv::Mat & result, double h)
1144 do_fill_holes(Image input, Image result, double n_stddevs)
1146 return _IMP_em2d.do_fill_holes(*args)
1148 def do_combined_fill_holes_and_threshold(*args):
1150 do_combined_fill_holes_and_threshold(cv::Mat & m, cv::Mat & result, double n_stddevs, double threshold=0.0)
1151 do_combined_fill_holes_and_threshold(cv::Mat & m, cv::Mat & result, double n_stddevs)
1152 do_combined_fill_holes_and_threshold(Image input, Image result, double n_stddevs)
1154 return _IMP_em2d.do_combined_fill_holes_and_threshold(*args)
1156 def do_extend_borders(*args):
1158 do_extend_borders(cv::Mat & orig, cv::Mat & dst, unsigned int pix)
1159 do_extend_borders(Image im1, Image im2, unsigned int pix)
1161 return _IMP_em2d.do_extend_borders(*args)
1163 def do_segmentation(*args):
1165 do_segmentation(cv::Mat const & m, cv::Mat & result, SegmentationParameters params)
1166 do_segmentation(Image input, Image result, SegmentationParameters params)
1168 return _IMP_em2d.do_segmentation(*args)
1170 def do_remove_small_objects(*args):
1172 do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage, int background=0, int foreground=1)
1173 do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage, int background=0)
1174 do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage)
1175 do_remove_small_objects(Image input, double percentage, int background=0, int foreground=1)
1176 do_remove_small_objects(Image input, double percentage, int background=0)
1177 do_remove_small_objects(Image input, double percentage)
1179 return _IMP_em2d.do_remove_small_objects(*args)
1182 """do_subtract_images(Image first, Image second, Image result)"""
1183 return _IMP_em2d.do_subtract_images(first, second, result)
1185 def add_noise(*args):
1187 add_noise(cv::Mat & v, double op1, double op2, IMP::String const & mode, double df=3)
1188 add_noise(cv::Mat & v, double op1, double op2, IMP::String const & mode)
1189 add_noise(cv::Mat & v, double op1, double op2)
1190 add_noise(Image im1, double op1, double op2, IMP::String const & mode, double df=3)
1191 add_noise(Image im1, double op1, double op2, IMP::String const & mode)
1192 add_noise(Image im1, double op1, double op2)
1194 return _IMP_em2d.add_noise(*args)
1198 do_resample_polar(cv::Mat const & input, cv::Mat & resampled, PolarResamplingParameters polar_params)
1199 do_resample_polar(Image im1, Image im2, PolarResamplingParameters polar_params)
1201 return _IMP_em2d.do_resample_polar(*args)
1205 crop(cv::Mat const & m, IMP::IntPair const & center, int size) -> cv::Mat
1206 crop(Image img, IMP::IntPair const & center, int size)
1208 return _IMP_em2d.crop(*args)
1211 """apply_mean_outside_mask(Image img, double radius)"""
1212 return _IMP_em2d.apply_mean_outside_mask(img, radius)
1213 class RegistrationResult(object):
1214 """Proxy of C++ IMP::em2d::RegistrationResult class."""
1216 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1218 def __init__(self, *args):
1220 __init__(IMP::em2d::RegistrationResult self) -> RegistrationResult
1221 __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
1222 __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0, int image_index=0) -> RegistrationResult
1223 __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0) -> RegistrationResult
1224 __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift) -> RegistrationResult
1225 __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift, int projection_index=0, int image_index=0, IMP::String name) -> RegistrationResult
1226 __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift, int projection_index=0, int image_index=0) -> RegistrationResult
1227 __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift, int projection_index=0) -> RegistrationResult
1228 __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift) -> RegistrationResult
1229 __init__(IMP::em2d::RegistrationResult self, Rotation3D R) -> RegistrationResult
1231 this = _IMP_em2d.new_RegistrationResult(*args)
1233 self.this.append(this)
1234 except __builtin__.Exception:
1238 """get_phi(RegistrationResult self) -> double"""
1239 return _IMP_em2d.RegistrationResult_get_phi(self)
1242 def get_theta(self):
1243 """get_theta(RegistrationResult self) -> double"""
1244 return _IMP_em2d.RegistrationResult_get_theta(self)
1248 """get_psi(RegistrationResult self) -> double"""
1249 return _IMP_em2d.RegistrationResult_get_psi(self)
1252 def get_shift(self):
1253 """get_shift(RegistrationResult self) -> Vector2D"""
1254 return _IMP_em2d.RegistrationResult_get_shift(self)
1257 def get_shift_3d(self):
1258 """get_shift_3d(RegistrationResult self) -> Vector3D"""
1259 return _IMP_em2d.RegistrationResult_get_shift_3d(self)
1262 def get_projection_index(self):
1263 """get_projection_index(RegistrationResult self) -> int"""
1264 return _IMP_em2d.RegistrationResult_get_projection_index(self)
1267 def set_projection_index(self, index):
1268 """set_projection_index(RegistrationResult self, int index)"""
1269 return _IMP_em2d.RegistrationResult_set_projection_index(self, index)
1272 def get_image_index(self):
1273 """get_image_index(RegistrationResult self) -> int"""
1274 return _IMP_em2d.RegistrationResult_get_image_index(self)
1277 def set_image_index(self, index):
1278 """set_image_index(RegistrationResult self, int index)"""
1279 return _IMP_em2d.RegistrationResult_set_image_index(self, index)
1283 """get_name(RegistrationResult self) -> IMP::String"""
1284 return _IMP_em2d.RegistrationResult_get_name(self)
1288 """get_ccc(RegistrationResult self) -> double"""
1289 return _IMP_em2d.RegistrationResult_get_ccc(self)
1292 def set_ccc(self, ccc):
1293 """set_ccc(RegistrationResult self, double ccc)"""
1294 return _IMP_em2d.RegistrationResult_set_ccc(self, ccc)
1297 def get_score(self):
1298 """get_score(RegistrationResult self) -> double"""
1299 return _IMP_em2d.RegistrationResult_get_score(self)
1302 def set_score(self, Score):
1303 """set_score(RegistrationResult self, double Score)"""
1304 return _IMP_em2d.RegistrationResult_set_score(self, Score)
1307 def set_rotation(self, *args):
1309 set_rotation(RegistrationResult self, double phi, double theta, double psi)
1310 set_rotation(RegistrationResult self, Rotation3D R)
1312 return _IMP_em2d.RegistrationResult_set_rotation(self, *args)
1315 def set_shift(self, shift):
1316 """set_shift(RegistrationResult self, Vector2D shift)"""
1317 return _IMP_em2d.RegistrationResult_set_shift(self, shift)
1320 def set_name(self, name):
1321 """set_name(RegistrationResult self, IMP::String name)"""
1322 return _IMP_em2d.RegistrationResult_set_name(self, name)
1325 def add_in_plane_transformation(self, t):
1326 """add_in_plane_transformation(RegistrationResult self, Transformation2D t)"""
1327 return _IMP_em2d.RegistrationResult_add_in_plane_transformation(self, t)
1330 def show(self, *args):
1332 show(RegistrationResult self, _ostream out)
1333 show(RegistrationResult self)
1335 return _IMP_em2d.RegistrationResult_show(self, *args)
1338 def write(self, *args):
1340 write(RegistrationResult self, _ostream out)
1341 write(RegistrationResult self)
1343 return _IMP_em2d.RegistrationResult_write(self, *args)
1346 def write_comment_line(self, *args):
1348 write_comment_line(RegistrationResult self, _ostream out)
1349 write_comment_line(RegistrationResult self)
1351 return _IMP_em2d.RegistrationResult_write_comment_line(self, *args)
1355 """read(RegistrationResult self, IMP::String const & s)"""
1356 return _IMP_em2d.RegistrationResult_read(self, s)
1359 def set_random_registration(self, index, maximum_shift):
1360 """set_random_registration(RegistrationResult self, unsigned int index, double maximum_shift)"""
1361 return _IMP_em2d.RegistrationResult_set_random_registration(self, index, maximum_shift)
1364 def get_rotation(self):
1365 """get_rotation(RegistrationResult self) -> Rotation3D"""
1366 return _IMP_em2d.RegistrationResult_get_rotation(self)
1369 def set_in_image(self, header):
1370 """set_in_image(RegistrationResult self, ImageHeader header)"""
1371 return _IMP_em2d.RegistrationResult_set_in_image(self, header)
1374 def read_from_image(self, header):
1375 """read_from_image(RegistrationResult self, ImageHeader header)"""
1376 return _IMP_em2d.RegistrationResult_read_from_image(self, header)
1379 def get_is_optimized_result(self):
1380 """get_is_optimized_result(RegistrationResult self) -> bool"""
1381 return _IMP_em2d.RegistrationResult_get_is_optimized_result(self)
1383 __swig_destroy__ = _IMP_em2d.delete_RegistrationResult
1384 __del__ =
lambda self:
None
1387 """__str__(RegistrationResult self) -> std::string"""
1388 return _IMP_em2d.RegistrationResult___str__(self)
1392 """__repr__(RegistrationResult self) -> std::string"""
1393 return _IMP_em2d.RegistrationResult___repr__(self)
1395 RegistrationResult_swigregister = _IMP_em2d.RegistrationResult_swigregister
1396 RegistrationResult_swigregister(RegistrationResult)
1400 """read_registration_results(IMP::String const & filename) -> IMP::em2d::RegistrationResults"""
1401 return _IMP_em2d.read_registration_results(filename)
1404 """write_registration_results(IMP::String filename, IMP::em2d::RegistrationResults const & results)"""
1405 return _IMP_em2d.write_registration_results(filename, results)
1409 get_random_registration_results(unsigned int n, double maximum_shift=5.0) -> IMP::em2d::RegistrationResults
1410 get_random_registration_results(unsigned int n) -> IMP::em2d::RegistrationResults
1412 return _IMP_em2d.get_random_registration_results(n, maximum_shift)
1415 """get_evenly_distributed_registration_results(unsigned int n_projections) -> IMP::em2d::RegistrationResults"""
1416 return _IMP_em2d.get_evenly_distributed_registration_results(n_projections)
1417 class SpiderImageReaderWriter(ImageReaderWriter):
1418 """Proxy of C++ IMP::em2d::SpiderImageReaderWriter class."""
1420 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1421 filename_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_filename__get, _IMP_em2d.SpiderImageReaderWriter_filename__set)
1422 skip_type_check_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_skip_type_check__get, _IMP_em2d.SpiderImageReaderWriter_skip_type_check__set)
1423 force_reversed_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_force_reversed__get, _IMP_em2d.SpiderImageReaderWriter_force_reversed__set)
1424 skip_extra_checkings_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__get, _IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__set)
1426 def __init__(self, *args):
1428 __init__(IMP::em2d::SpiderImageReaderWriter self) -> SpiderImageReaderWriter
1429 __init__(IMP::em2d::SpiderImageReaderWriter self, IMP::String const & filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderImageReaderWriter
1431 this = _IMP_em2d.new_SpiderImageReaderWriter(*args)
1433 self.this.append(this)
1434 except __builtin__.Exception:
1438 """__str__(SpiderImageReaderWriter self) -> std::string"""
1439 return _IMP_em2d.SpiderImageReaderWriter___str__(self)
1443 """__repr__(SpiderImageReaderWriter self) -> std::string"""
1444 return _IMP_em2d.SpiderImageReaderWriter___repr__(self)
1449 return _object_cast_to_SpiderImageReaderWriter(o)
1451 SpiderImageReaderWriter_swigregister = _IMP_em2d.SpiderImageReaderWriter_swigregister
1452 SpiderImageReaderWriter_swigregister(SpiderImageReaderWriter)
1454 class JPGImageReaderWriter(ImageReaderWriter):
1455 """Proxy of C++ IMP::em2d::JPGImageReaderWriter class."""
1457 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1460 """__init__(IMP::em2d::JPGImageReaderWriter self) -> JPGImageReaderWriter"""
1461 this = _IMP_em2d.new_JPGImageReaderWriter()
1463 self.this.append(this)
1464 except __builtin__.Exception:
1468 """__str__(JPGImageReaderWriter self) -> std::string"""
1469 return _IMP_em2d.JPGImageReaderWriter___str__(self)
1473 """__repr__(JPGImageReaderWriter self) -> std::string"""
1474 return _IMP_em2d.JPGImageReaderWriter___repr__(self)
1479 return _object_cast_to_JPGImageReaderWriter(o)
1481 JPGImageReaderWriter_swigregister = _IMP_em2d.JPGImageReaderWriter_swigregister
1482 JPGImageReaderWriter_swigregister(JPGImageReaderWriter)
1484 class TIFFImageReaderWriter(ImageReaderWriter):
1485 """Proxy of C++ IMP::em2d::TIFFImageReaderWriter class."""
1487 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1490 """__init__(IMP::em2d::TIFFImageReaderWriter self) -> TIFFImageReaderWriter"""
1491 this = _IMP_em2d.new_TIFFImageReaderWriter()
1493 self.this.append(this)
1494 except __builtin__.Exception:
1498 """__str__(TIFFImageReaderWriter self) -> std::string"""
1499 return _IMP_em2d.TIFFImageReaderWriter___str__(self)
1503 """__repr__(TIFFImageReaderWriter self) -> std::string"""
1504 return _IMP_em2d.TIFFImageReaderWriter___repr__(self)
1509 return _object_cast_to_TIFFImageReaderWriter(o)
1511 TIFFImageReaderWriter_swigregister = _IMP_em2d.TIFFImageReaderWriter_swigregister
1512 TIFFImageReaderWriter_swigregister(TIFFImageReaderWriter)
1516 """do_matrix_to_image_flip(cv::Mat & m)"""
1517 return _IMP_em2d.do_matrix_to_image_flip(m)
1520 """get_autocorrelation2d_no_preprocessing(cv::Mat const & M, cv::Mat & corr)"""
1521 return _IMP_em2d.get_autocorrelation2d_no_preprocessing(M, corr)
1525 get_autocorrelation2d(Image im1, Image im2)
1526 get_autocorrelation2d(cv::Mat const & m, cv::Mat & corr)
1528 return _IMP_em2d.get_autocorrelation2d(*args)
1532 get_correlation2d(Image im1, Image im2, Image corr)
1533 get_correlation2d(cv::Mat const & A, cv::Mat const & B, cv::Mat & corr)
1535 return _IMP_em2d.get_correlation2d(*args)
1538 """get_correlation2d_no_preprocessing(cv::Mat const & M1, cv::Mat const & M2, cv::Mat & corr)"""
1539 return _IMP_em2d.get_correlation2d_no_preprocessing(M1, M2, corr)
1542 """get_fft_using_optimal_size(cv::Mat const & m, cv::Mat & M)"""
1543 return _IMP_em2d.get_fft_using_optimal_size(m, M)
1546 """get_spectrum(cv::Mat const & m, cv::Mat & real, cv::Mat & imag)"""
1547 return _IMP_em2d.get_spectrum(m, real, imag)
1550 """get_rotation_error(RegistrationResult rr1, RegistrationResult rr2) -> double"""
1551 return _IMP_em2d.get_rotation_error(rr1, rr2)
1554 """get_shift_error(RegistrationResult rr1, RegistrationResult rr2) -> double"""
1555 return _IMP_em2d.get_shift_error(rr1, rr2)
1557 def get_average_rotation_error(correct_RRs, computed_RRs):
1558 """get_average_rotation_error(IMP::em2d::RegistrationResults const & correct_RRs, IMP::em2d::RegistrationResults const & computed_RRs) -> double"""
1559 return _IMP_em2d.get_average_rotation_error(correct_RRs, computed_RRs)
1561 def get_average_shift_error(correct_RRs, computed_RRs):
1562 """get_average_shift_error(IMP::em2d::RegistrationResults const & correct_RRs, IMP::em2d::RegistrationResults const & computed_RRs) -> double"""
1563 return _IMP_em2d.get_average_shift_error(correct_RRs, computed_RRs)
1567 get_cross_correlation_coefficient(Image im1, Image im2) -> double
1568 get_cross_correlation_coefficient(cv::Mat const & m1, cv::Mat const & m2) -> double
1570 return _IMP_em2d.get_cross_correlation_coefficient(*args)
1573 """get_global_score(IMP::em2d::RegistrationResults const & RRs) -> double"""
1574 return _IMP_em2d.get_global_score(RRs)
1576 """Proxy of C++ IMP::em2d::ScoreFunction class."""
1578 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1580 def __init__(self, *args, **kwargs):
1581 raise AttributeError(
"No constructor defined - class is abstract")
1583 def get_score(self, image, projection):
1584 """get_score(ScoreFunction self, Image image, Image projection) -> double"""
1585 return _IMP_em2d.ScoreFunction_get_score(self, image, projection)
1588 def set_variance_image(self, var):
1589 """set_variance_image(ScoreFunction self, Image var)"""
1590 return _IMP_em2d.ScoreFunction_set_variance_image(self, var)
1593 def get_version_info(self):
1594 """get_version_info(ScoreFunction self) -> VersionInfo"""
1595 return _IMP_em2d.ScoreFunction_get_version_info(self)
1599 """__str__(ScoreFunction self) -> std::string"""
1600 return _IMP_em2d.ScoreFunction___str__(self)
1604 """__repr__(ScoreFunction self) -> std::string"""
1605 return _IMP_em2d.ScoreFunction___repr__(self)
1610 return _object_cast_to_ScoreFunction(o)
1612 ScoreFunction_swigregister = _IMP_em2d.ScoreFunction_swigregister
1613 ScoreFunction_swigregister(ScoreFunction)
1615 class ChiSquaredScore(ScoreFunction):
1616 """Proxy of C++ IMP::em2d::ChiSquaredScore class."""
1618 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1621 """__init__(IMP::em2d::ChiSquaredScore self) -> ChiSquaredScore"""
1622 this = _IMP_em2d.new_ChiSquaredScore()
1624 self.this.append(this)
1625 except __builtin__.Exception:
1629 """__str__(ChiSquaredScore self) -> std::string"""
1630 return _IMP_em2d.ChiSquaredScore___str__(self)
1634 """__repr__(ChiSquaredScore self) -> std::string"""
1635 return _IMP_em2d.ChiSquaredScore___repr__(self)
1640 return _object_cast_to_ChiSquaredScore(o)
1642 __swig_destroy__ = _IMP_em2d.delete_ChiSquaredScore
1643 __del__ =
lambda self:
None
1644 ChiSquaredScore_swigregister = _IMP_em2d.ChiSquaredScore_swigregister
1645 ChiSquaredScore_swigregister(ChiSquaredScore)
1647 class EM2DScore(ScoreFunction):
1648 """Proxy of C++ IMP::em2d::EM2DScore class."""
1650 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1653 """__init__(IMP::em2d::EM2DScore self) -> EM2DScore"""
1654 this = _IMP_em2d.new_EM2DScore()
1656 self.this.append(this)
1657 except __builtin__.Exception:
1661 """__str__(EM2DScore self) -> std::string"""
1662 return _IMP_em2d.EM2DScore___str__(self)
1666 """__repr__(EM2DScore self) -> std::string"""
1667 return _IMP_em2d.EM2DScore___repr__(self)
1672 return _object_cast_to_EM2DScore(o)
1674 __swig_destroy__ = _IMP_em2d.delete_EM2DScore
1675 __del__ =
lambda self:
None
1676 EM2DScore_swigregister = _IMP_em2d.EM2DScore_swigregister
1677 EM2DScore_swigregister(EM2DScore)
1679 class MeanAbsoluteDifference(ScoreFunction):
1680 """Proxy of C++ IMP::em2d::MeanAbsoluteDifference class."""
1682 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1685 """__init__(IMP::em2d::MeanAbsoluteDifference self) -> MeanAbsoluteDifference"""
1686 this = _IMP_em2d.new_MeanAbsoluteDifference()
1688 self.this.append(this)
1689 except __builtin__.Exception:
1693 """__str__(MeanAbsoluteDifference self) -> std::string"""
1694 return _IMP_em2d.MeanAbsoluteDifference___str__(self)
1698 """__repr__(MeanAbsoluteDifference self) -> std::string"""
1699 return _IMP_em2d.MeanAbsoluteDifference___repr__(self)
1704 return _object_cast_to_MeanAbsoluteDifference(o)
1706 __swig_destroy__ = _IMP_em2d.delete_MeanAbsoluteDifference
1707 __del__ =
lambda self:
None
1708 MeanAbsoluteDifference_swigregister = _IMP_em2d.MeanAbsoluteDifference_swigregister
1709 MeanAbsoluteDifference_swigregister(MeanAbsoluteDifference)
1713 """read_selection_file(IMP::String fn) -> IMP::Strings"""
1714 return _IMP_em2d.read_selection_file(fn)
1717 """create_filenames(unsigned long number, IMP::String basic_name, IMP::String extension) -> IMP::Strings"""
1718 return _IMP_em2d.create_filenames(number, basic_name, extension)
1720 """Proxy of C++ IMP::em2d::ProjectionParameters class."""
1722 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1724 def __init__(self, *args):
1726 __init__(IMP::em2d::ProjectionParameters self) -> ProjectionParameters
1727 __init__(IMP::em2d::ProjectionParameters self, Model m, ParticleIndex id) -> ProjectionParameters
1728 __init__(IMP::em2d::ProjectionParameters self, _ParticleAdaptor d) -> ProjectionParameters
1730 this = _IMP_em2d.new_ProjectionParameters(*args)
1732 self.this.append(this)
1733 except __builtin__.Exception:
1736 def show(self, *args):
1738 show(ProjectionParameters self, _ostream out)
1739 show(ProjectionParameters self)
1741 return _IMP_em2d.ProjectionParameters_show(self, *args)
1744 def setup_particle(*args):
1746 setup_particle(Model m, ParticleIndex pi) -> ProjectionParameters
1747 setup_particle(_ParticleAdaptor decorator) -> ProjectionParameters
1749 return _IMP_em2d.ProjectionParameters_setup_particle(*args)
1751 setup_particle = staticmethod(setup_particle)
1752 __swig_destroy__ = _IMP_em2d.delete_ProjectionParameters
1753 __del__ =
lambda self:
None
1756 """get_keys() -> IMP::FloatKeys const &"""
1757 return _IMP_em2d.ProjectionParameters_get_keys()
1759 get_keys = staticmethod(get_keys)
1761 def set_proper_ranges_for_keys(self, m, min_translation_values, max_translation_values):
1762 """set_proper_ranges_for_keys(ProjectionParameters self, Model m, Vector3D min_translation_values, Vector3D max_translation_values)"""
1763 return _IMP_em2d.ProjectionParameters_set_proper_ranges_for_keys(self, m, min_translation_values, max_translation_values)
1766 def get_is_setup(*args):
1768 get_is_setup(_ParticleAdaptor p) -> bool
1769 get_is_setup(Model m, ParticleIndex pi) -> bool
1771 return _IMP_em2d.ProjectionParameters_get_is_setup(*args)
1773 get_is_setup = staticmethod(get_is_setup)
1775 def get_parameters_optimized(self):
1776 """get_parameters_optimized(ProjectionParameters self) -> bool"""
1777 return _IMP_em2d.ProjectionParameters_get_parameters_optimized(self)
1780 def get_translation(self):
1781 """get_translation(ProjectionParameters self) -> Vector3D"""
1782 return _IMP_em2d.ProjectionParameters_get_translation(self)
1785 def set_translation(self, v):
1786 """set_translation(ProjectionParameters self, Vector3D v)"""
1787 return _IMP_em2d.ProjectionParameters_set_translation(self, v)
1790 def get_rotation(self):
1791 """get_rotation(ProjectionParameters self) -> Rotation3D"""
1792 return _IMP_em2d.ProjectionParameters_get_rotation(self)
1795 def set_rotation(self, R):
1796 """set_rotation(ProjectionParameters self, Rotation3D R)"""
1797 return _IMP_em2d.ProjectionParameters_set_rotation(self, R)
1800 def set_parameters_optimized(self, tf):
1801 """set_parameters_optimized(ProjectionParameters self, bool tf)"""
1802 return _IMP_em2d.ProjectionParameters_set_parameters_optimized(self, tf)
1805 def get_quaternion_1(self):
1806 """get_quaternion_1(ProjectionParameters self) -> double"""
1807 return _IMP_em2d.ProjectionParameters_get_quaternion_1(self)
1810 def set_quaternion_1(self, t):
1811 """set_quaternion_1(ProjectionParameters self, double t)"""
1812 return _IMP_em2d.ProjectionParameters_set_quaternion_1(self, t)
1815 def get_quaternion_2(self):
1816 """get_quaternion_2(ProjectionParameters self) -> double"""
1817 return _IMP_em2d.ProjectionParameters_get_quaternion_2(self)
1820 def set_quaternion_2(self, t):
1821 """set_quaternion_2(ProjectionParameters self, double t)"""
1822 return _IMP_em2d.ProjectionParameters_set_quaternion_2(self, t)
1825 def get_quaternion_3(self):
1826 """get_quaternion_3(ProjectionParameters self) -> double"""
1827 return _IMP_em2d.ProjectionParameters_get_quaternion_3(self)
1830 def set_quaternion_3(self, t):
1831 """set_quaternion_3(ProjectionParameters self, double t)"""
1832 return _IMP_em2d.ProjectionParameters_set_quaternion_3(self, t)
1835 def get_quaternion_4(self):
1836 """get_quaternion_4(ProjectionParameters self) -> double"""
1837 return _IMP_em2d.ProjectionParameters_get_quaternion_4(self)
1840 def set_quaternion_4(self, t):
1841 """set_quaternion_4(ProjectionParameters self, double t)"""
1842 return _IMP_em2d.ProjectionParameters_set_quaternion_4(self, t)
1845 def get_translation_x(self):
1846 """get_translation_x(ProjectionParameters self) -> double"""
1847 return _IMP_em2d.ProjectionParameters_get_translation_x(self)
1850 def set_translation_x(self, t):
1851 """set_translation_x(ProjectionParameters self, double t)"""
1852 return _IMP_em2d.ProjectionParameters_set_translation_x(self, t)
1855 def get_translation_y(self):
1856 """get_translation_y(ProjectionParameters self) -> double"""
1857 return _IMP_em2d.ProjectionParameters_get_translation_y(self)
1860 def set_translation_y(self, t):
1861 """set_translation_y(ProjectionParameters self, double t)"""
1862 return _IMP_em2d.ProjectionParameters_set_translation_y(self, t)
1865 def add_attribute(self, *args):
1867 add_attribute(ProjectionParameters self, FloatKey k, IMP::Float v, bool opt)
1868 add_attribute(ProjectionParameters self, FloatKey a0, IMP::Float a1)
1869 add_attribute(ProjectionParameters self, IntKey a0, IMP::Int a1)
1870 add_attribute(ProjectionParameters self, StringKey a0, IMP::String a1)
1871 add_attribute(ProjectionParameters self, ParticleIndexKey a0, Particle a1)
1872 add_attribute(ProjectionParameters self, ObjectKey a0, Object a1)
1874 return _IMP_em2d.ProjectionParameters_add_attribute(self, *args)
1877 def get_value(self, *args):
1879 get_value(ProjectionParameters self, FloatKey a0) -> IMP::Float
1880 get_value(ProjectionParameters self, IntKey a0) -> IMP::Int
1881 get_value(ProjectionParameters self, StringKey a0) -> IMP::String
1882 get_value(ProjectionParameters self, ParticleIndexKey a0) -> Particle
1883 get_value(ProjectionParameters self, ObjectKey a0) -> Object
1885 return _IMP_em2d.ProjectionParameters_get_value(self, *args)
1888 def set_value(self, *args):
1890 set_value(ProjectionParameters self, FloatKey a0, IMP::Float a1)
1891 set_value(ProjectionParameters self, IntKey a0, IMP::Int a1)
1892 set_value(ProjectionParameters self, StringKey a0, IMP::String a1)
1893 set_value(ProjectionParameters self, ParticleIndexKey a0, Particle a1)
1894 set_value(ProjectionParameters self, ObjectKey a0, Object a1)
1896 return _IMP_em2d.ProjectionParameters_set_value(self, *args)
1899 def remove_attribute(self, *args):
1901 remove_attribute(ProjectionParameters self, FloatKey a0)
1902 remove_attribute(ProjectionParameters self, IntKey a0)
1903 remove_attribute(ProjectionParameters self, StringKey a0)
1904 remove_attribute(ProjectionParameters self, ParticleIndexKey a0)
1905 remove_attribute(ProjectionParameters self, ObjectKey a0)
1907 return _IMP_em2d.ProjectionParameters_remove_attribute(self, *args)
1910 def has_attribute(self, *args):
1912 has_attribute(ProjectionParameters self, FloatKey a0) -> bool
1913 has_attribute(ProjectionParameters self, IntKey a0) -> bool
1914 has_attribute(ProjectionParameters self, StringKey a0) -> bool
1915 has_attribute(ProjectionParameters self, ParticleIndexKey a0) -> bool
1916 has_attribute(ProjectionParameters self, ObjectKey a0) -> bool
1918 return _IMP_em2d.ProjectionParameters_has_attribute(self, *args)
1921 def get_derivative(self, a0):
1922 """get_derivative(ProjectionParameters self, FloatKey a0) -> double"""
1923 return _IMP_em2d.ProjectionParameters_get_derivative(self, a0)
1927 """get_name(ProjectionParameters self) -> std::string"""
1928 return _IMP_em2d.ProjectionParameters_get_name(self)
1931 def clear_caches(self):
1932 """clear_caches(ProjectionParameters self)"""
1933 return _IMP_em2d.ProjectionParameters_clear_caches(self)
1936 def set_name(self, a0):
1937 """set_name(ProjectionParameters self, std::string a0)"""
1938 return _IMP_em2d.ProjectionParameters_set_name(self, a0)
1942 """set_check_level(ProjectionParameters self, IMP::CheckLevel a0)"""
1943 return _IMP_em2d.ProjectionParameters_set_check_level(self, a0)
1946 def add_to_derivative(self, a0, a1, a2):
1947 """add_to_derivative(ProjectionParameters self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1948 return _IMP_em2d.ProjectionParameters_add_to_derivative(self, a0, a1, a2)
1951 def set_is_optimized(self, a0, a1):
1952 """set_is_optimized(ProjectionParameters self, FloatKey a0, bool a1)"""
1953 return _IMP_em2d.ProjectionParameters_set_is_optimized(self, a0, a1)
1956 def get_is_optimized(self, a0):
1957 """get_is_optimized(ProjectionParameters self, FloatKey a0) -> bool"""
1958 return _IMP_em2d.ProjectionParameters_get_is_optimized(self, a0)
1962 """get_check_level(ProjectionParameters self) -> IMP::CheckLevel"""
1963 return _IMP_em2d.ProjectionParameters_get_check_level(self)
1966 def __eq__(self, *args):
1968 __eq__(ProjectionParameters self, ProjectionParameters o) -> bool
1969 __eq__(ProjectionParameters self, Particle d) -> bool
1971 return _IMP_em2d.ProjectionParameters___eq__(self, *args)
1974 def __ne__(self, *args):
1976 __ne__(ProjectionParameters self, ProjectionParameters o) -> bool
1977 __ne__(ProjectionParameters self, Particle d) -> bool
1979 return _IMP_em2d.ProjectionParameters___ne__(self, *args)
1982 def __le__(self, *args):
1984 __le__(ProjectionParameters self, ProjectionParameters o) -> bool
1985 __le__(ProjectionParameters self, Particle d) -> bool
1987 return _IMP_em2d.ProjectionParameters___le__(self, *args)
1990 def __lt__(self, *args):
1992 __lt__(ProjectionParameters self, ProjectionParameters o) -> bool
1993 __lt__(ProjectionParameters self, Particle d) -> bool
1995 return _IMP_em2d.ProjectionParameters___lt__(self, *args)
1998 def __ge__(self, *args):
2000 __ge__(ProjectionParameters self, ProjectionParameters o) -> bool
2001 __ge__(ProjectionParameters self, Particle d) -> bool
2003 return _IMP_em2d.ProjectionParameters___ge__(self, *args)
2006 def __gt__(self, *args):
2008 __gt__(ProjectionParameters self, ProjectionParameters o) -> bool
2009 __gt__(ProjectionParameters self, Particle d) -> bool
2011 return _IMP_em2d.ProjectionParameters___gt__(self, *args)
2015 """__hash__(ProjectionParameters self) -> std::size_t"""
2016 return _IMP_em2d.ProjectionParameters___hash__(self)
2020 """__str__(ProjectionParameters self) -> std::string"""
2021 return _IMP_em2d.ProjectionParameters___str__(self)
2025 """__repr__(ProjectionParameters self) -> std::string"""
2026 return _IMP_em2d.ProjectionParameters___repr__(self)
2028 ProjectionParameters_swigregister = _IMP_em2d.ProjectionParameters_swigregister
2029 ProjectionParameters_swigregister(ProjectionParameters)
2031 def ProjectionParameters_setup_particle(*args):
2033 setup_particle(Model m, ParticleIndex pi) -> ProjectionParameters
2034 ProjectionParameters_setup_particle(_ParticleAdaptor decorator) -> ProjectionParameters
2036 return _IMP_em2d.ProjectionParameters_setup_particle(*args)
2038 def ProjectionParameters_get_keys():
2039 """ProjectionParameters_get_keys() -> IMP::FloatKeys const &"""
2040 return _IMP_em2d.ProjectionParameters_get_keys()
2042 def ProjectionParameters_get_is_setup(*args):
2044 get_is_setup(_ParticleAdaptor p) -> bool
2045 ProjectionParameters_get_is_setup(Model m, ParticleIndex pi) -> bool
2047 return _IMP_em2d.ProjectionParameters_get_is_setup(*args)
2050 def __lshift__(out, n):
2051 """__lshift__(_ostream out, ProjectionParameters n) -> _ostream"""
2052 return _IMP_em2d.__lshift__(out, n)
2054 """Proxy of C++ IMP::em2d::ProjectionParametersScoreState class."""
2056 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2058 def __init__(self, p):
2059 """__init__(IMP::em2d::ProjectionParametersScoreState self, Particle p) -> ProjectionParametersScoreState"""
2060 this = _IMP_em2d.new_ProjectionParametersScoreState(p)
2062 self.this.append(this)
2063 except __builtin__.Exception:
2066 def do_before_evaluate(self):
2067 """do_before_evaluate(ProjectionParametersScoreState self)"""
2068 return _IMP_em2d.ProjectionParametersScoreState_do_before_evaluate(self)
2071 def do_after_evaluate(self, da):
2072 """do_after_evaluate(ProjectionParametersScoreState self, DerivativeAccumulator da)"""
2073 return _IMP_em2d.ProjectionParametersScoreState_do_after_evaluate(self, da)
2076 def do_get_inputs(self):
2077 """do_get_inputs(ProjectionParametersScoreState self) -> IMP::ModelObjectsTemp"""
2078 return _IMP_em2d.ProjectionParametersScoreState_do_get_inputs(self)
2081 def do_get_outputs(self):
2082 """do_get_outputs(ProjectionParametersScoreState self) -> IMP::ModelObjectsTemp"""
2083 return _IMP_em2d.ProjectionParametersScoreState_do_get_outputs(self)
2086 def get_version_info(self):
2087 """get_version_info(ProjectionParametersScoreState self) -> VersionInfo"""
2088 return _IMP_em2d.ProjectionParametersScoreState_get_version_info(self)
2092 """__str__(ProjectionParametersScoreState self) -> std::string"""
2093 return _IMP_em2d.ProjectionParametersScoreState___str__(self)
2097 """__repr__(ProjectionParametersScoreState self) -> std::string"""
2098 return _IMP_em2d.ProjectionParametersScoreState___repr__(self)
2103 return _object_cast_to_ProjectionParametersScoreState(o)
2105 ProjectionParametersScoreState_swigregister = _IMP_em2d.ProjectionParametersScoreState_swigregister
2106 ProjectionParametersScoreState_swigregister(ProjectionParametersScoreState)
2108 class ProjectionMask(object):
2109 """Proxy of C++ IMP::em2d::ProjectionMask class."""
2111 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2113 def __init__(self, *args, **kwargs):
2114 raise AttributeError(
"No constructor defined")
2116 def apply(self, m, v):
2117 """apply(ProjectionMask self, cv::Mat & m, Vector2D v)"""
2118 return _IMP_em2d.ProjectionMask_apply(self, m, v)
2121 def show(self, *args):
2123 show(ProjectionMask self, _ostream out)
2124 show(ProjectionMask self)
2126 return _IMP_em2d.ProjectionMask_show(self, *args)
2128 __swig_destroy__ = _IMP_em2d.delete_ProjectionMask
2129 __del__ =
lambda self:
None
2132 """__str__(ProjectionMask self) -> std::string"""
2133 return _IMP_em2d.ProjectionMask___str__(self)
2137 """__repr__(ProjectionMask self) -> std::string"""
2138 return _IMP_em2d.ProjectionMask___repr__(self)
2140 ProjectionMask_swigregister = _IMP_em2d.ProjectionMask_swigregister
2141 ProjectionMask_swigregister(ProjectionMask)
2145 """do_place(cv::Mat & mask, cv::Mat & m, Vector2D v)"""
2146 return _IMP_em2d.do_place(mask, m, v)
2147 class MasksManager(object):
2148 """Proxy of C++ IMP::em2d::MasksManager class."""
2150 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2152 def __init__(self, *args):
2154 __init__(IMP::em2d::MasksManager self) -> MasksManager
2155 __init__(IMP::em2d::MasksManager self, double resolution, double pixelsize) -> MasksManager
2157 this = _IMP_em2d.new_MasksManager(*args)
2159 self.this.append(this)
2160 except __builtin__.Exception:
2163 def setup_kernel(self, resolution, pixelsize):
2164 """setup_kernel(MasksManager self, double resolution, double pixelsize)"""
2165 return _IMP_em2d.MasksManager_setup_kernel(self, resolution, pixelsize)
2168 def create_masks(self, ps):
2169 """create_masks(MasksManager self, IMP::ParticlesTemp const & ps)"""
2170 return _IMP_em2d.MasksManager_create_masks(self, ps)
2173 def create_mask(self, mass):
2174 """create_mask(MasksManager self, double mass)"""
2175 return _IMP_em2d.MasksManager_create_mask(self, mass)
2178 def find_mask(self, mass):
2179 """find_mask(MasksManager self, double mass) -> IMP::em2d::ProjectionMaskPtr"""
2180 return _IMP_em2d.MasksManager_find_mask(self, mass)
2183 def show(self, *args):
2185 show(MasksManager self, _ostream out)
2186 show(MasksManager self)
2188 return _IMP_em2d.MasksManager_show(self, *args)
2191 def get_number_of_masks(self):
2192 """get_number_of_masks(MasksManager self) -> unsigned int"""
2193 return _IMP_em2d.MasksManager_get_number_of_masks(self)
2195 __swig_destroy__ = _IMP_em2d.delete_MasksManager
2196 __del__ =
lambda self:
None
2199 """__str__(MasksManager self) -> std::string"""
2200 return _IMP_em2d.MasksManager___str__(self)
2204 """__repr__(MasksManager self) -> std::string"""
2205 return _IMP_em2d.MasksManager___repr__(self)
2207 MasksManager_swigregister = _IMP_em2d.MasksManager_swigregister
2208 MasksManager_swigregister(MasksManager)
2210 class ProjectingParameters(object):
2211 """Proxy of C++ IMP::em2d::ProjectingParameters class."""
2213 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2214 pixel_size = _swig_property(_IMP_em2d.ProjectingParameters_pixel_size_get, _IMP_em2d.ProjectingParameters_pixel_size_set)
2215 resolution = _swig_property(_IMP_em2d.ProjectingParameters_resolution_get, _IMP_em2d.ProjectingParameters_resolution_set)
2217 def __init__(self, *args):
2219 __init__(IMP::em2d::ProjectingParameters self) -> ProjectingParameters
2220 __init__(IMP::em2d::ProjectingParameters self, double ps, double res) -> ProjectingParameters
2222 this = _IMP_em2d.new_ProjectingParameters(*args)
2224 self.this.append(this)
2225 except __builtin__.Exception:
2228 def show(self, *args):
2230 show(ProjectingParameters self, _ostream out)
2231 show(ProjectingParameters self)
2233 return _IMP_em2d.ProjectingParameters_show(self, *args)
2237 """__str__(ProjectingParameters self) -> std::string"""
2238 return _IMP_em2d.ProjectingParameters___str__(self)
2242 """__repr__(ProjectingParameters self) -> std::string"""
2243 return _IMP_em2d.ProjectingParameters___repr__(self)
2245 __swig_destroy__ = _IMP_em2d.delete_ProjectingParameters
2246 __del__ =
lambda self:
None
2247 ProjectingParameters_swigregister = _IMP_em2d.ProjectingParameters_swigregister
2248 ProjectingParameters_swigregister(ProjectingParameters)
2250 class ProjectingOptions(ProjectingParameters):
2251 """Proxy of C++ IMP::em2d::ProjectingOptions class."""
2253 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2254 save_images = _swig_property(_IMP_em2d.ProjectingOptions_save_images_get, _IMP_em2d.ProjectingOptions_save_images_set)
2255 normalize = _swig_property(_IMP_em2d.ProjectingOptions_normalize_get, _IMP_em2d.ProjectingOptions_normalize_set)
2256 clear_matrix_before_projecting = _swig_property(_IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_get, _IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_set)
2258 def __init__(self, *args):
2260 __init__(IMP::em2d::ProjectingOptions self) -> ProjectingOptions
2261 __init__(IMP::em2d::ProjectingOptions self, double ps, double res) -> ProjectingOptions
2262 __init__(IMP::em2d::ProjectingOptions self, double ps, double res, ImageReaderWriter irw) -> ProjectingOptions
2264 this = _IMP_em2d.new_ProjectingOptions(*args)
2266 self.this.append(this)
2267 except __builtin__.Exception:
2270 def show(self, *args):
2272 show(ProjectingOptions self, _ostream out)
2273 show(ProjectingOptions self)
2275 return _IMP_em2d.ProjectingOptions_show(self, *args)
2279 """__str__(ProjectingOptions self) -> std::string"""
2280 return _IMP_em2d.ProjectingOptions___str__(self)
2284 """__repr__(ProjectingOptions self) -> std::string"""
2285 return _IMP_em2d.ProjectingOptions___repr__(self)
2287 __swig_destroy__ = _IMP_em2d.delete_ProjectingOptions
2288 __del__ =
lambda self:
None
2289 ProjectingOptions_swigregister = _IMP_em2d.ProjectingOptions_swigregister
2290 ProjectingOptions_swigregister(ProjectingOptions)
2295 get_projections(IMP::ParticlesTemp const & ps, IMP::algebra::SphericalVector3Ds const & vs, int rows, int cols, ProjectingOptions options, IMP::Strings names) -> IMP::em2d::Images
2296 get_projections(IMP::ParticlesTemp const & ps, IMP::algebra::SphericalVector3Ds const & vs, int rows, int cols, ProjectingOptions options) -> IMP::em2d::Images
2297 get_projections(IMP::ParticlesTemp const & ps, IMP::em2d::RegistrationResults const & registration_values, int rows, int cols, ProjectingOptions options, IMP::Strings names) -> IMP::em2d::Images
2298 get_projections(IMP::ParticlesTemp const & ps, IMP::em2d::RegistrationResults const & registration_values, int rows, int cols, ProjectingOptions options) -> IMP::em2d::Images
2300 return _IMP_em2d.get_projections(*args)
2304 get_projection(Image img, IMP::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks, IMP::String name)
2305 get_projection(Image img, IMP::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks)
2306 get_projection(Image img, IMP::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options)
2308 return _IMP_em2d.get_projection(*args)
2311 """do_project_particles(IMP::ParticlesTemp const & ps, cv::Mat & m2, Rotation3D R, Vector3D translation, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks)"""
2312 return _IMP_em2d.do_project_particles(ps, m2, R, translation, options, masks)
2315 """create_evenly_distributed_projections(IMP::ParticlesTemp const & ps, unsigned int n, ProjectingOptions options) -> IMP::em2d::Images"""
2316 return _IMP_em2d.create_evenly_distributed_projections(ps, n, options)
2320 do_project_vectors(IMP::algebra::Vector3Ds const & ps, Rotation3D R, Vector3D translation) -> IMP::algebra::Vector2Ds
2321 do_project_vectors(IMP::algebra::Vector3Ds const & ps, Rotation3D R, Vector3D translation, Vector3D center) -> IMP::algebra::Vector2Ds
2323 return _IMP_em2d.do_project_vectors(*args)
2326 """get_enclosing_image_size(IMP::ParticlesTemp const & ps, double pixel_size, unsigned int slack) -> unsigned int"""
2327 return _IMP_em2d.get_enclosing_image_size(ps, pixel_size, slack)
2331 get_complete_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2332 get_complete_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2334 return _IMP_em2d.get_complete_alignment(input, m_to_align, apply)
2338 get_rotational_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2339 get_rotational_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2341 return _IMP_em2d.get_rotational_alignment(input, m_to_align, apply)
2345 get_translational_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2346 get_translational_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2348 return _IMP_em2d.get_translational_alignment(input, m_to_align, apply)
2352 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
2353 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
2355 return _IMP_em2d.get_complete_alignment_no_preprocessing(input, INPUT, POLAR1, m_to_align, POLAR2, apply)
2358 """get_rotational_alignment_no_preprocessing(cv::Mat const & POLAR1, cv::Mat const & POLAR2) -> ResultAlign2D"""
2359 return _IMP_em2d.get_rotational_alignment_no_preprocessing(POLAR1, POLAR2)
2362 """get_translational_alignment_no_preprocessing(cv::Mat const & M1, cv::Mat const & M2) -> ResultAlign2D"""
2363 return _IMP_em2d.get_translational_alignment_no_preprocessing(M1, M2)
2366 """get_complete_alignment_with_centers_no_preprocessing(Vector2D center1, Vector2D center2, cv::Mat const & AUTOC_POLAR1, cv::Mat const & AUTOC_POLAR2) -> ResultAlign2D"""
2367 return _IMP_em2d.get_complete_alignment_with_centers_no_preprocessing(center1, center2, AUTOC_POLAR1, AUTOC_POLAR2)
2371 write_vectors_as_pdb(IMP::algebra::Vector2Ds const vs, IMP::String const filename)
2372 write_vectors_as_pdb(IMP::algebra::Vector3Ds const vs, IMP::String const filename)
2374 return _IMP_em2d.write_vectors_as_pdb(*args)
2375 class Em2DRestraintParameters(ProjectingParameters):
2376 """Proxy of C++ IMP::em2d::Em2DRestraintParameters class."""
2378 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2379 n_projections = _swig_property(_IMP_em2d.Em2DRestraintParameters_n_projections_get, _IMP_em2d.Em2DRestraintParameters_n_projections_set)
2380 coarse_registration_method = _swig_property(_IMP_em2d.Em2DRestraintParameters_coarse_registration_method_get, _IMP_em2d.Em2DRestraintParameters_coarse_registration_method_set)
2381 save_match_images = _swig_property(_IMP_em2d.Em2DRestraintParameters_save_match_images_get, _IMP_em2d.Em2DRestraintParameters_save_match_images_set)
2382 optimization_steps = _swig_property(_IMP_em2d.Em2DRestraintParameters_optimization_steps_get, _IMP_em2d.Em2DRestraintParameters_optimization_steps_set)
2383 simplex_initial_length = _swig_property(_IMP_em2d.Em2DRestraintParameters_simplex_initial_length_get, _IMP_em2d.Em2DRestraintParameters_simplex_initial_length_set)
2384 simplex_minimum_size = _swig_property(_IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_get, _IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_set)
2386 def __init__(self, *args):
2388 __init__(IMP::em2d::Em2DRestraintParameters self) -> Em2DRestraintParameters
2389 __init__(IMP::em2d::Em2DRestraintParameters self, double ps, double res, unsigned int n_proj=20) -> Em2DRestraintParameters
2390 __init__(IMP::em2d::Em2DRestraintParameters self, double ps, double res) -> Em2DRestraintParameters
2392 this = _IMP_em2d.new_Em2DRestraintParameters(*args)
2394 self.this.append(this)
2395 except __builtin__.Exception:
2398 def show(self, *args):
2400 show(Em2DRestraintParameters self, _ostream out)
2401 show(Em2DRestraintParameters self)
2403 return _IMP_em2d.Em2DRestraintParameters_show(self, *args)
2407 """__str__(Em2DRestraintParameters self) -> std::string"""
2408 return _IMP_em2d.Em2DRestraintParameters___str__(self)
2412 """__repr__(Em2DRestraintParameters self) -> std::string"""
2413 return _IMP_em2d.Em2DRestraintParameters___repr__(self)
2415 __swig_destroy__ = _IMP_em2d.delete_Em2DRestraintParameters
2416 __del__ =
lambda self:
None
2417 Em2DRestraintParameters_swigregister = _IMP_em2d.Em2DRestraintParameters_swigregister
2418 Em2DRestraintParameters_swigregister(Em2DRestraintParameters)
2419 cvar = _IMP_em2d.cvar
2420 ALIGN2D_NO_PREPROCESSING = cvar.ALIGN2D_NO_PREPROCESSING
2421 ALIGN2D_PREPROCESSING = cvar.ALIGN2D_PREPROCESSING
2422 ALIGN2D_WITH_CENTERS = cvar.ALIGN2D_WITH_CENTERS
2425 """Proxy of C++ IMP::em2d::ProjectionFinder class."""
2427 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2430 """__init__(IMP::em2d::ProjectionFinder self) -> ProjectionFinder"""
2431 this = _IMP_em2d.new_ProjectionFinder()
2433 self.this.append(this)
2434 except __builtin__.Exception:
2437 def setup(self, score_function, params):
2438 """setup(ProjectionFinder self, ScoreFunction score_function, Em2DRestraintParameters params)"""
2439 return _IMP_em2d.ProjectionFinder_setup(self, score_function, params)
2442 def set_subjects(self, subjects):
2443 """set_subjects(ProjectionFinder self, IMP::em2d::Images const & subjects)"""
2444 return _IMP_em2d.ProjectionFinder_set_subjects(self, subjects)
2447 def set_projections(self, projections):
2448 """set_projections(ProjectionFinder self, IMP::em2d::Images const & projections)"""
2449 return _IMP_em2d.ProjectionFinder_set_projections(self, projections)
2452 def set_variance_images(self, variances):
2453 """set_variance_images(ProjectionFinder self, IMP::em2d::Images const & variances)"""
2454 return _IMP_em2d.ProjectionFinder_set_variance_images(self, variances)
2457 def set_model_particles(self, ps):
2458 """set_model_particles(ProjectionFinder self, IMP::ParticlesTemp const & ps)"""
2459 return _IMP_em2d.ProjectionFinder_set_model_particles(self, ps)
2462 def set_save_match_images(self, x):
2463 """set_save_match_images(ProjectionFinder self, bool x)"""
2464 return _IMP_em2d.ProjectionFinder_set_save_match_images(self, x)
2467 def get_save_match_images(self):
2468 """get_save_match_images(ProjectionFinder self) -> bool"""
2469 return _IMP_em2d.ProjectionFinder_get_save_match_images(self)
2472 def set_fast_mode(self, n):
2473 """set_fast_mode(ProjectionFinder self, unsigned int n)"""
2474 return _IMP_em2d.ProjectionFinder_set_fast_mode(self, n)
2477 def get_registration_results(self):
2478 """get_registration_results(ProjectionFinder self) -> IMP::em2d::RegistrationResults"""
2479 return _IMP_em2d.ProjectionFinder_get_registration_results(self)
2482 def get_coarse_registration(self):
2483 """get_coarse_registration(ProjectionFinder self)"""
2484 return _IMP_em2d.ProjectionFinder_get_coarse_registration(self)
2487 def get_complete_registration(self):
2488 """get_complete_registration(ProjectionFinder self)"""
2489 return _IMP_em2d.ProjectionFinder_get_complete_registration(self)
2493 """get_global_score(ProjectionFinder self) -> double"""
2494 return _IMP_em2d.ProjectionFinder_get_global_score(self)
2497 def show(self, out):
2498 """show(ProjectionFinder self, _ostream out)"""
2499 return _IMP_em2d.ProjectionFinder_show(self, out)
2502 def get_preprocessing_time(self):
2503 """get_preprocessing_time(ProjectionFinder self) -> double"""
2504 return _IMP_em2d.ProjectionFinder_get_preprocessing_time(self)
2507 def get_coarse_registration_time(self):
2508 """get_coarse_registration_time(ProjectionFinder self) -> double"""
2509 return _IMP_em2d.ProjectionFinder_get_coarse_registration_time(self)
2512 def get_fine_registration_time(self):
2513 """get_fine_registration_time(ProjectionFinder self) -> double"""
2514 return _IMP_em2d.ProjectionFinder_get_fine_registration_time(self)
2517 def get_number_of_subjects(self):
2518 """get_number_of_subjects(ProjectionFinder self) -> unsigned int"""
2519 return _IMP_em2d.ProjectionFinder_get_number_of_subjects(self)
2522 def set_number_of_class_averages_members(self, n_members):
2523 """set_number_of_class_averages_members(ProjectionFinder self, IMP::Ints n_members)"""
2524 return _IMP_em2d.ProjectionFinder_set_number_of_class_averages_members(self, n_members)
2527 def get_number_of_projections(self):
2528 """get_number_of_projections(ProjectionFinder self) -> unsigned int"""
2529 return _IMP_em2d.ProjectionFinder_get_number_of_projections(self)
2532 def get_version_info(self):
2533 """get_version_info(ProjectionFinder self) -> VersionInfo"""
2534 return _IMP_em2d.ProjectionFinder_get_version_info(self)
2538 """__str__(ProjectionFinder self) -> std::string"""
2539 return _IMP_em2d.ProjectionFinder___str__(self)
2543 """__repr__(ProjectionFinder self) -> std::string"""
2544 return _IMP_em2d.ProjectionFinder___repr__(self)
2549 return _object_cast_to_ProjectionFinder(o)
2551 ProjectionFinder_swigregister = _IMP_em2d.ProjectionFinder_swigregister
2552 ProjectionFinder_swigregister(ProjectionFinder)
2555 """Proxy of C++ IMP::em2d::Em2DRestraint class."""
2557 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2559 def __init__(self, m):
2560 """__init__(IMP::em2d::Em2DRestraint self, Model m) -> Em2DRestraint"""
2561 this = _IMP_em2d.new_Em2DRestraint(m)
2563 self.this.append(this)
2564 except __builtin__.Exception:
2567 def setup(self, score_function, params):
2568 """setup(Em2DRestraint self, ScoreFunction score_function, Em2DRestraintParameters params)"""
2569 return _IMP_em2d.Em2DRestraint_setup(self, score_function, params)
2572 def set_particles(self, particles_container):
2573 """set_particles(Em2DRestraint self, SingletonContainer particles_container)"""
2574 return _IMP_em2d.Em2DRestraint_set_particles(self, particles_container)
2577 def set_images(self, em_images):
2578 """set_images(Em2DRestraint self, IMP::em2d::Images const em_images)"""
2579 return _IMP_em2d.Em2DRestraint_set_images(self, em_images)
2582 def set_variance_images(self, variance_images):
2583 """set_variance_images(Em2DRestraint self, IMP::em2d::Images const variance_images)"""
2584 return _IMP_em2d.Em2DRestraint_set_variance_images(self, variance_images)
2587 def set_fast_mode(self, n):
2588 """set_fast_mode(Em2DRestraint self, unsigned int n)"""
2589 return _IMP_em2d.Em2DRestraint_set_fast_mode(self, n)
2592 def set_coarse_registration_mode(self, opt):
2593 """set_coarse_registration_mode(Em2DRestraint self, bool opt)"""
2594 return _IMP_em2d.Em2DRestraint_set_coarse_registration_mode(self, opt)
2597 def get_registration_results(self):
2598 """get_registration_results(Em2DRestraint self) -> IMP::em2d::RegistrationResults"""
2599 return _IMP_em2d.Em2DRestraint_get_registration_results(self)
2602 def do_get_inputs(self):
2603 """do_get_inputs(Em2DRestraint self) -> IMP::ModelObjectsTemp"""
2604 return _IMP_em2d.Em2DRestraint_do_get_inputs(self)
2607 def get_version_info(self):
2608 """get_version_info(Em2DRestraint self) -> VersionInfo"""
2609 return _IMP_em2d.Em2DRestraint_get_version_info(self)
2613 """__str__(Em2DRestraint self) -> std::string"""
2614 return _IMP_em2d.Em2DRestraint___str__(self)
2618 """__repr__(Em2DRestraint self) -> std::string"""
2619 return _IMP_em2d.Em2DRestraint___repr__(self)
2624 return _object_cast_to_Em2DRestraint(o)
2626 Em2DRestraint_swigregister = _IMP_em2d.Em2DRestraint_swigregister
2627 Em2DRestraint_swigregister(Em2DRestraint)
2629 class ClusterSet(object):
2630 """Proxy of C++ IMP::em2d::ClusterSet class."""
2632 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2634 def __init__(self, N):
2635 """__init__(IMP::em2d::ClusterSet self, unsigned int N) -> ClusterSet"""
2636 this = _IMP_em2d.new_ClusterSet(N)
2638 self.this.append(this)
2639 except __builtin__.Exception:
2642 def do_join_clusters(self, cluster_id1, cluster_id2, distance_between_clusters):
2643 """do_join_clusters(ClusterSet self, unsigned int cluster_id1, unsigned int cluster_id2, double distance_between_clusters)"""
2644 return _IMP_em2d.ClusterSet_do_join_clusters(self, cluster_id1, cluster_id2, distance_between_clusters)
2647 def get_cluster_elements(self, id):
2648 """get_cluster_elements(ClusterSet self, unsigned int id) -> IMP::Ints"""
2649 return _IMP_em2d.ClusterSet_get_cluster_elements(self, id)
2652 def get_clusters_below_cutoff(self, cutoff):
2653 """get_clusters_below_cutoff(ClusterSet self, double cutoff) -> IMP::Ints"""
2654 return _IMP_em2d.ClusterSet_get_clusters_below_cutoff(self, cutoff)
2657 def get_cluster_formed_at_step(self, step):
2658 """get_cluster_formed_at_step(ClusterSet self, unsigned int step) -> IMP::Ints"""
2659 return _IMP_em2d.ClusterSet_get_cluster_formed_at_step(self, step)
2662 def get_distance_at_step(self, step):
2663 """get_distance_at_step(ClusterSet self, unsigned int step) -> double"""
2664 return _IMP_em2d.ClusterSet_get_distance_at_step(self, step)
2667 def get_id_for_cluster_at_step(self, step):
2668 """get_id_for_cluster_at_step(ClusterSet self, unsigned int step) -> unsigned int"""
2669 return _IMP_em2d.ClusterSet_get_id_for_cluster_at_step(self, step)
2672 def get_linkage_matrix(self):
2673 """get_linkage_matrix(ClusterSet self) -> IMP::FloatsList"""
2674 return _IMP_em2d.ClusterSet_get_linkage_matrix(self)
2677 def get_linkage_matrix_in_matlab_format(self):
2678 """get_linkage_matrix_in_matlab_format(ClusterSet self) -> IMP::FloatsList"""
2679 return _IMP_em2d.ClusterSet_get_linkage_matrix_in_matlab_format(self)
2682 def get_number_of_steps(self):
2683 """get_number_of_steps(ClusterSet self) -> unsigned int"""
2684 return _IMP_em2d.ClusterSet_get_number_of_steps(self)
2687 def show(self, out):
2688 """show(ClusterSet self, _ostream out)"""
2689 return _IMP_em2d.ClusterSet_show(self, out)
2693 """__str__(ClusterSet self) -> std::string"""
2694 return _IMP_em2d.ClusterSet___str__(self)
2698 """__repr__(ClusterSet self) -> std::string"""
2699 return _IMP_em2d.ClusterSet___repr__(self)
2701 __swig_destroy__ = _IMP_em2d.delete_ClusterSet
2702 __del__ =
lambda self:
None
2703 ClusterSet_swigregister = _IMP_em2d.ClusterSet_swigregister
2704 ClusterSet_swigregister(ClusterSet)
2706 class SingleLinkage(object):
2707 """Proxy of C++ IMP::em2d::SingleLinkage class."""
2709 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2712 """__init__(IMP::em2d::SingleLinkage self) -> SingleLinkage"""
2713 this = _IMP_em2d.new_SingleLinkage()
2715 self.this.append(this)
2716 except __builtin__.Exception:
2719 def __call__(self, id1, id2, cluster_set, distances):
2720 """__call__(SingleLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2721 return _IMP_em2d.SingleLinkage___call__(self, id1, id2, cluster_set, distances)
2724 def show(self, out):
2725 """show(SingleLinkage self, _ostream out)"""
2726 return _IMP_em2d.SingleLinkage_show(self, out)
2730 """__str__(SingleLinkage self) -> std::string"""
2731 return _IMP_em2d.SingleLinkage___str__(self)
2735 """__repr__(SingleLinkage self) -> std::string"""
2736 return _IMP_em2d.SingleLinkage___repr__(self)
2738 __swig_destroy__ = _IMP_em2d.delete_SingleLinkage
2739 __del__ =
lambda self:
None
2740 SingleLinkage_swigregister = _IMP_em2d.SingleLinkage_swigregister
2741 SingleLinkage_swigregister(SingleLinkage)
2743 class CompleteLinkage(object):
2744 """Proxy of C++ IMP::em2d::CompleteLinkage class."""
2746 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2749 """__init__(IMP::em2d::CompleteLinkage self) -> CompleteLinkage"""
2750 this = _IMP_em2d.new_CompleteLinkage()
2752 self.this.append(this)
2753 except __builtin__.Exception:
2756 def __call__(self, id1, id2, cluster_set, distances):
2757 """__call__(CompleteLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2758 return _IMP_em2d.CompleteLinkage___call__(self, id1, id2, cluster_set, distances)
2761 def show(self, out):
2762 """show(CompleteLinkage self, _ostream out)"""
2763 return _IMP_em2d.CompleteLinkage_show(self, out)
2767 """__str__(CompleteLinkage self) -> std::string"""
2768 return _IMP_em2d.CompleteLinkage___str__(self)
2772 """__repr__(CompleteLinkage self) -> std::string"""
2773 return _IMP_em2d.CompleteLinkage___repr__(self)
2775 __swig_destroy__ = _IMP_em2d.delete_CompleteLinkage
2776 __del__ =
lambda self:
None
2777 CompleteLinkage_swigregister = _IMP_em2d.CompleteLinkage_swigregister
2778 CompleteLinkage_swigregister(CompleteLinkage)
2780 class AverageDistanceLinkage(object):
2781 """Proxy of C++ IMP::em2d::AverageDistanceLinkage class."""
2783 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2786 """__init__(IMP::em2d::AverageDistanceLinkage self) -> AverageDistanceLinkage"""
2787 this = _IMP_em2d.new_AverageDistanceLinkage()
2789 self.this.append(this)
2790 except __builtin__.Exception:
2793 def __call__(self, id1, id2, cluster_set, distances):
2794 """__call__(AverageDistanceLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2795 return _IMP_em2d.AverageDistanceLinkage___call__(self, id1, id2, cluster_set, distances)
2798 def show(self, out):
2799 """show(AverageDistanceLinkage self, _ostream out)"""
2800 return _IMP_em2d.AverageDistanceLinkage_show(self, out)
2804 """__str__(AverageDistanceLinkage self) -> std::string"""
2805 return _IMP_em2d.AverageDistanceLinkage___str__(self)
2809 """__repr__(AverageDistanceLinkage self) -> std::string"""
2810 return _IMP_em2d.AverageDistanceLinkage___repr__(self)
2812 __swig_destroy__ = _IMP_em2d.delete_AverageDistanceLinkage
2813 __del__ =
lambda self:
None
2814 AverageDistanceLinkage_swigregister = _IMP_em2d.AverageDistanceLinkage_swigregister
2815 AverageDistanceLinkage_swigregister(AverageDistanceLinkage)
2818 """Proxy of C++ IMP::em2d::CollisionCrossSection class."""
2820 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2822 def __init__(self, n_projections, resolution, pixel_size, projection_image_size):
2823 """__init__(IMP::em2d::CollisionCrossSection self, unsigned int n_projections, double resolution, double pixel_size, double projection_image_size) -> CollisionCrossSection"""
2824 this = _IMP_em2d.new_CollisionCrossSection(n_projections, resolution, pixel_size, projection_image_size)
2826 self.this.append(this)
2827 except __builtin__.Exception:
2830 def set_model_particles(self, ps):
2831 """set_model_particles(CollisionCrossSection self, IMP::ParticlesTemp const & ps)"""
2832 return _IMP_em2d.CollisionCrossSection_set_model_particles(self, ps)
2836 """get_ccs(CollisionCrossSection self) -> double"""
2837 return _IMP_em2d.CollisionCrossSection_get_ccs(self)
2840 def show(self, out):
2841 """show(CollisionCrossSection self, _ostream out)"""
2842 return _IMP_em2d.CollisionCrossSection_show(self, out)
2845 def get_version_info(self):
2846 """get_version_info(CollisionCrossSection self) -> VersionInfo"""
2847 return _IMP_em2d.CollisionCrossSection_get_version_info(self)
2851 """__str__(CollisionCrossSection self) -> std::string"""
2852 return _IMP_em2d.CollisionCrossSection___str__(self)
2856 """__repr__(CollisionCrossSection self) -> std::string"""
2857 return _IMP_em2d.CollisionCrossSection___repr__(self)
2862 return _object_cast_to_CollisionCrossSection(o)
2864 CollisionCrossSection_swigregister = _IMP_em2d.CollisionCrossSection_swigregister
2865 CollisionCrossSection_swigregister(CollisionCrossSection)
2868 """Proxy of C++ IMP::em2d::GridStates class."""
2870 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2872 def __init__(self, *args):
2874 __init__(IMP::em2d::GridStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations, IMP::String const & name) -> GridStates
2875 __init__(IMP::em2d::GridStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations) -> GridStates
2877 this = _IMP_em2d.new_GridStates(*args)
2879 self.this.append(this)
2880 except __builtin__.Exception:
2883 def get_position(self, i):
2884 """get_position(GridStates self, unsigned int i) -> Vector3D"""
2885 return _IMP_em2d.GridStates_get_position(self, i)
2888 def get_orientation(self, i):
2889 """get_orientation(GridStates self, unsigned int i) -> Rotation3D"""
2890 return _IMP_em2d.GridStates_get_orientation(self, i)
2893 def get_version_info(self):
2894 """get_version_info(GridStates self) -> VersionInfo"""
2895 return _IMP_em2d.GridStates_get_version_info(self)
2899 """__str__(GridStates self) -> std::string"""
2900 return _IMP_em2d.GridStates___str__(self)
2904 """__repr__(GridStates self) -> std::string"""
2905 return _IMP_em2d.GridStates___repr__(self)
2910 return _object_cast_to_GridStates(o)
2912 GridStates_swigregister = _IMP_em2d.GridStates_swigregister
2913 GridStates_swigregister(GridStates)
2915 class ProjectionStates(GridStates):
2916 """Proxy of C++ IMP::em2d::ProjectionStates class."""
2918 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2920 def __init__(self, *args):
2922 __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
2923 __init__(IMP::em2d::ProjectionStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations, IMP::em2d::Images const & projections) -> ProjectionStates
2925 this = _IMP_em2d.new_ProjectionStates(*args)
2927 self.this.append(this)
2928 except __builtin__.Exception:
2932 """get_projection(ProjectionStates self, unsigned int i) -> Image"""
2933 return _IMP_em2d.ProjectionStates_get_projection(self, i)
2937 """__str__(ProjectionStates self) -> std::string"""
2938 return _IMP_em2d.ProjectionStates___str__(self)
2942 """__repr__(ProjectionStates self) -> std::string"""
2943 return _IMP_em2d.ProjectionStates___repr__(self)
2948 return _object_cast_to_ProjectionStates(o)
2950 ProjectionStates_swigregister = _IMP_em2d.ProjectionStates_swigregister
2951 ProjectionStates_swigregister(ProjectionStates)
2954 """Proxy of C++ IMP::em2d::DistanceFilter class."""
2956 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2958 def __init__(self, subset_to_act_on, subset_to_restrain, ps_table, max_distance):
2959 """__init__(IMP::em2d::DistanceFilter self, Subset subset_to_act_on, Subset subset_to_restrain, ParticleStatesTable ps_table, double max_distance) -> DistanceFilter"""
2960 this = _IMP_em2d.new_DistanceFilter(subset_to_act_on, subset_to_restrain, ps_table, max_distance)
2962 self.this.append(this)
2963 except __builtin__.Exception:
2966 def show(self, *args):
2968 show(DistanceFilter self, _ostream out)
2969 show(DistanceFilter self)
2971 return _IMP_em2d.DistanceFilter_show(self, *args)
2974 def get_version_info(self):
2975 """get_version_info(DistanceFilter self) -> VersionInfo"""
2976 return _IMP_em2d.DistanceFilter_get_version_info(self)
2980 """__str__(DistanceFilter self) -> std::string"""
2981 return _IMP_em2d.DistanceFilter___str__(self)
2985 """__repr__(DistanceFilter self) -> std::string"""
2986 return _IMP_em2d.DistanceFilter___repr__(self)
2991 return _object_cast_to_DistanceFilter(o)
2993 DistanceFilter_swigregister = _IMP_em2d.DistanceFilter_swigregister
2994 DistanceFilter_swigregister(DistanceFilter)
2997 """Proxy of C++ IMP::em2d::DistanceFilterTable class."""
2999 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3001 def __init__(self, subset_to_act_on, ps_table, max_distance):
3002 """__init__(IMP::em2d::DistanceFilterTable self, Subset subset_to_act_on, ParticleStatesTable ps_table, double max_distance) -> DistanceFilterTable"""
3003 this = _IMP_em2d.new_DistanceFilterTable(subset_to_act_on, ps_table, max_distance)
3005 self.this.append(this)
3006 except __builtin__.Exception:
3009 def show(self, *args):
3011 show(DistanceFilterTable self, _ostream out)
3012 show(DistanceFilterTable self)
3014 return _IMP_em2d.DistanceFilterTable_show(self, *args)
3017 def get_version_info(self):
3018 """get_version_info(DistanceFilterTable self) -> VersionInfo"""
3019 return _IMP_em2d.DistanceFilterTable_get_version_info(self)
3023 """__str__(DistanceFilterTable self) -> std::string"""
3024 return _IMP_em2d.DistanceFilterTable___str__(self)
3028 """__repr__(DistanceFilterTable self) -> std::string"""
3029 return _IMP_em2d.DistanceFilterTable___repr__(self)
3034 return _object_cast_to_DistanceFilterTable(o)
3036 DistanceFilterTable_swigregister = _IMP_em2d.DistanceFilterTable_swigregister
3037 DistanceFilterTable_swigregister(DistanceFilterTable)
3039 class IntsOrder(object):
3040 """Proxy of C++ IMP::em2d::IntsOrder class."""
3042 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3043 __repr__ = _swig_repr
3045 def __call__(self, a, b):
3046 """__call__(IntsOrder self, IMP::Ints const & a, IMP::Ints const & b) -> bool"""
3047 return _IMP_em2d.IntsOrder___call__(self, a, b)
3051 """__init__(IMP::em2d::IntsOrder self) -> IntsOrder"""
3052 this = _IMP_em2d.new_IntsOrder()
3054 self.this.append(this)
3055 except __builtin__.Exception:
3057 __swig_destroy__ = _IMP_em2d.delete_IntsOrder
3058 __del__ =
lambda self:
None
3059 IntsOrder_swigregister = _IMP_em2d.IntsOrder_swigregister
3060 IntsOrder_swigregister(IntsOrder)
3063 """Proxy of C++ IMP::em2d::RigidBodiesImageFitRestraint class."""
3065 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3067 def get_version_info(self):
3068 """get_version_info(RigidBodiesImageFitRestraint self) -> VersionInfo"""
3069 return _IMP_em2d.RigidBodiesImageFitRestraint_get_version_info(self)
3072 def __init__(self, scf, rbs, img):
3073 """__init__(IMP::em2d::RigidBodiesImageFitRestraint self, ScoreFunction scf, IMP::core::RigidBodies const & rbs, Image img) -> RigidBodiesImageFitRestraint"""
3074 this = _IMP_em2d.new_RigidBodiesImageFitRestraint(scf, rbs, img)
3076 self.this.append(this)
3077 except __builtin__.Exception:
3080 def set_projecting_parameters(self, p):
3081 """set_projecting_parameters(RigidBodiesImageFitRestraint self, ProjectingParameters p)"""
3082 return _IMP_em2d.RigidBodiesImageFitRestraint_set_projecting_parameters(self, p)
3085 def set_orientations(self, rb, rots):
3086 """set_orientations(RigidBodiesImageFitRestraint self, RigidBody rb, IMP::algebra::Rotation3Ds const & rots)"""
3087 return _IMP_em2d.RigidBodiesImageFitRestraint_set_orientations(self, rb, rots)
3090 def get_number_of_masks(self, rb):
3091 """get_number_of_masks(RigidBodiesImageFitRestraint self, RigidBody rb) -> unsigned int"""
3092 return _IMP_em2d.RigidBodiesImageFitRestraint_get_number_of_masks(self, rb)
3096 """__str__(RigidBodiesImageFitRestraint self) -> std::string"""
3097 return _IMP_em2d.RigidBodiesImageFitRestraint___str__(self)
3101 """__repr__(RigidBodiesImageFitRestraint self) -> std::string"""
3102 return _IMP_em2d.RigidBodiesImageFitRestraint___repr__(self)
3107 return _object_cast_to_RigidBodiesImageFitRestraint(o)
3109 RigidBodiesImageFitRestraint_swigregister = _IMP_em2d.RigidBodiesImageFitRestraint_swigregister
3110 RigidBodiesImageFitRestraint_swigregister(RigidBodiesImageFitRestraint)
3114 """get_unique_index(Rotation3D rot) -> IMP::Ints"""
3115 return _IMP_em2d.get_unique_index(rot)
3117 """Proxy of C++ IMP::em2d::RelativePositionMover class."""
3119 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3121 def __init__(self, d, max_translation, max_rotation):
3122 """__init__(IMP::em2d::RelativePositionMover self, RigidBody d, IMP::Float max_translation, IMP::Float max_rotation) -> RelativePositionMover"""
3123 this = _IMP_em2d.new_RelativePositionMover(d, max_translation, max_rotation)
3125 self.this.append(this)
3126 except __builtin__.Exception:
3129 def add_internal_transformations(self, d, transforms):
3130 """add_internal_transformations(RelativePositionMover self, RigidBody d, IMP::algebra::Transformation3Ds transforms)"""
3131 return _IMP_em2d.RelativePositionMover_add_internal_transformations(self, d, transforms)
3134 def set_random_move_probability(self, p):
3135 """set_random_move_probability(RelativePositionMover self, IMP::Float p)"""
3136 return _IMP_em2d.RelativePositionMover_set_random_move_probability(self, p)
3140 """__str__(RelativePositionMover self) -> std::string"""
3141 return _IMP_em2d.RelativePositionMover___str__(self)
3145 """__repr__(RelativePositionMover self) -> std::string"""
3146 return _IMP_em2d.RelativePositionMover___repr__(self)
3151 return _object_cast_to_RelativePositionMover(o)
3153 RelativePositionMover_swigregister = _IMP_em2d.RelativePositionMover_swigregister
3154 RelativePositionMover_swigregister(RelativePositionMover)
3157 """Proxy of C++ IMP::em2d::DummyRestraint class."""
3159 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3161 def __init__(self, p, q):
3162 """__init__(IMP::em2d::DummyRestraint self, Particle p, Particle q) -> DummyRestraint"""
3163 this = _IMP_em2d.new_DummyRestraint(p, q)
3165 self.this.append(this)
3166 except __builtin__.Exception:
3169 def show(self, *args):
3171 show(DummyRestraint self, _ostream out)
3172 show(DummyRestraint self)
3174 return _IMP_em2d.DummyRestraint_show(self, *args)
3177 def do_get_inputs(self):
3178 """do_get_inputs(DummyRestraint self) -> IMP::ModelObjectsTemp"""
3179 return _IMP_em2d.DummyRestraint_do_get_inputs(self)
3182 def get_version_info(self):
3183 """get_version_info(DummyRestraint self) -> VersionInfo"""
3184 return _IMP_em2d.DummyRestraint_get_version_info(self)
3188 """__str__(DummyRestraint self) -> std::string"""
3189 return _IMP_em2d.DummyRestraint___str__(self)
3193 """__repr__(DummyRestraint self) -> std::string"""
3194 return _IMP_em2d.DummyRestraint___repr__(self)
3199 return _object_cast_to_DummyRestraint(o)
3201 DummyRestraint_swigregister = _IMP_em2d.DummyRestraint_swigregister
3202 DummyRestraint_swigregister(DummyRestraint)
3205 """Proxy of C++ IMP::em2d::ParticlesDummyRestraint class."""
3207 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3209 def __init__(self, sc):
3210 """__init__(IMP::em2d::ParticlesDummyRestraint self, SingletonContainer sc) -> ParticlesDummyRestraint"""
3211 this = _IMP_em2d.new_ParticlesDummyRestraint(sc)
3213 self.this.append(this)
3214 except __builtin__.Exception:
3217 def show(self, *args):
3219 show(ParticlesDummyRestraint self, _ostream out)
3220 show(ParticlesDummyRestraint self)
3222 return _IMP_em2d.ParticlesDummyRestraint_show(self, *args)
3225 def do_get_inputs(self):
3226 """do_get_inputs(ParticlesDummyRestraint self) -> IMP::ModelObjectsTemp"""
3227 return _IMP_em2d.ParticlesDummyRestraint_do_get_inputs(self)
3230 def get_version_info(self):
3231 """get_version_info(ParticlesDummyRestraint self) -> VersionInfo"""
3232 return _IMP_em2d.ParticlesDummyRestraint_get_version_info(self)
3236 """__str__(ParticlesDummyRestraint self) -> std::string"""
3237 return _IMP_em2d.ParticlesDummyRestraint___str__(self)
3241 """__repr__(ParticlesDummyRestraint self) -> std::string"""
3242 return _IMP_em2d.ParticlesDummyRestraint___repr__(self)
3247 return _object_cast_to_ParticlesDummyRestraint(o)
3249 ParticlesDummyRestraint_swigregister = _IMP_em2d.ParticlesDummyRestraint_swigregister
3250 ParticlesDummyRestraint_swigregister(ParticlesDummyRestraint)
3253 """Proxy of C++ IMP::em2d::PCAFitRestraint class."""
3255 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3257 def __init__(self, particles, image_files, pixel_size, resolution=10.0, projection_number=100, reuse_direction=False, n_components=1):
3259 __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
3260 __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
3261 __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size, double resolution=10.0, unsigned int projection_number=100) -> PCAFitRestraint
3262 __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size, double resolution=10.0) -> PCAFitRestraint
3263 __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size) -> PCAFitRestraint
3265 this = _IMP_em2d.new_PCAFitRestraint(particles, image_files, pixel_size, resolution, projection_number, reuse_direction, n_components)
3267 self.this.append(this)
3268 except __builtin__.Exception:
3271 def get_projection_number(self):
3272 """get_projection_number(PCAFitRestraint self) -> unsigned int"""
3273 return _IMP_em2d.PCAFitRestraint_get_projection_number(self)
3276 def set_projection_number(self, n):
3277 """set_projection_number(PCAFitRestraint self, unsigned int n)"""
3278 return _IMP_em2d.PCAFitRestraint_set_projection_number(self, n)
3281 def get_transformation(self, image_number):
3282 """get_transformation(PCAFitRestraint self, unsigned int image_number) -> Transformation3D"""
3283 return _IMP_em2d.PCAFitRestraint_get_transformation(self, image_number)
3287 """get_cross_correlation_coefficient(PCAFitRestraint self, unsigned int image_number) -> double"""
3288 return _IMP_em2d.PCAFitRestraint_get_cross_correlation_coefficient(self, image_number)
3291 def write_best_projections(self, file_name, evaluate=False):
3293 write_best_projections(PCAFitRestraint self, std::string file_name, bool evaluate=False)
3294 write_best_projections(PCAFitRestraint self, std::string file_name)
3296 return _IMP_em2d.PCAFitRestraint_write_best_projections(self, file_name, evaluate)
3299 def do_get_inputs(self):
3300 """do_get_inputs(PCAFitRestraint self) -> IMP::ModelObjectsTemp"""
3301 return _IMP_em2d.PCAFitRestraint_do_get_inputs(self)
3304 def get_version_info(self):
3305 """get_version_info(PCAFitRestraint self) -> VersionInfo"""
3306 return _IMP_em2d.PCAFitRestraint_get_version_info(self)
3310 """__str__(PCAFitRestraint self) -> std::string"""
3311 return _IMP_em2d.PCAFitRestraint___str__(self)
3315 """__repr__(PCAFitRestraint self) -> std::string"""
3316 return _IMP_em2d.PCAFitRestraint___repr__(self)
3321 return _object_cast_to_em2dPCAFitRestraint(o)
3323 PCAFitRestraint_swigregister = _IMP_em2d.PCAFitRestraint_swigregister
3324 PCAFitRestraint_swigregister(PCAFitRestraint)
3327 """Proxy of C++ std::pair<(IMP::algebra::Transformation2D,double)> class."""
3329 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3330 __repr__ = _swig_repr
3332 def __init__(self, *args):
3334 __init__(std::pair<(IMP::algebra::Transformation2D,double)> self) -> ResultAlign2D
3335 __init__(std::pair<(IMP::algebra::Transformation2D,double)> self, Transformation2D first, double second) -> ResultAlign2D
3336 __init__(std::pair<(IMP::algebra::Transformation2D,double)> self, ResultAlign2D p) -> ResultAlign2D
3338 this = _IMP_em2d.new_ResultAlign2D(*args)
3340 self.this.append(this)
3341 except __builtin__.Exception:
3343 first = _swig_property(_IMP_em2d.ResultAlign2D_first_get, _IMP_em2d.ResultAlign2D_first_set)
3344 second = _swig_property(_IMP_em2d.ResultAlign2D_second_get, _IMP_em2d.ResultAlign2D_second_set)
3348 return str((self.first, self.second))
3349 def __getitem__(self, index):
3354 def __setitem__(self, index, val):
3359 __swig_destroy__ = _IMP_em2d.delete_ResultAlign2D
3360 __del__ =
lambda self:
None
3361 ResultAlign2D_swigregister = _IMP_em2d.ResultAlign2D_swigregister
3362 ResultAlign2D_swigregister(ResultAlign2D)
3365 def _do_hierarchical_clustering_single_linkage(distances):
3366 """_do_hierarchical_clustering_single_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3367 return _IMP_em2d._do_hierarchical_clustering_single_linkage(distances)
3369 def _do_hierarchical_clustering_complete_linkage(distances):
3370 """_do_hierarchical_clustering_complete_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3371 return _IMP_em2d._do_hierarchical_clustering_complete_linkage(distances)
3373 def _do_hierarchical_clustering_average_distance_linkage(distances):
3374 """_do_hierarchical_clustering_average_distance_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3375 return _IMP_em2d._do_hierarchical_clustering_average_distance_linkage(distances)
3377 do_hierarchical_clustering_single_linkage = _do_hierarchical_clustering_single_linkage
3378 do_hierarchical_clustering_complete_linkage = _do_hierarchical_clustering_complete_linkage
3379 do_hierarchical_clustering_average_distance_linkage = _do_hierarchical_clustering_average_distance_linkage
3382 def get_module_version():
3383 """get_module_version() -> std::string const"""
3384 return _IMP_em2d.get_module_version()
3387 """get_example_path(std::string fname) -> std::string"""
3388 return _IMP_em2d.get_example_path(fname)
3391 """get_data_path(std::string fname) -> std::string"""
3392 return _IMP_em2d.get_data_path(fname)
3394 from .
import _version_check
3395 _version_check.check_version(get_module_version())
3396 __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.