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 ProjectionParametersList(l=[]):
649 return [ProjectionParameters(x)
for x
in l]
650 _plural_types.append(
"ProjectionParametersList")
653 _value_types.append(
"ProjectionParameters")
658 show(cv::Mat const & m, _ostream out)
659 show(cv::Mat const & m)
661 return _IMP_em2d.show(*args)
664 """write_matrix(cv::Mat & m, std::string name)"""
665 return _IMP_em2d.write_matrix(m, name)
667 """Proxy of C++ IMP::em2d::ImageReaderWriter class."""
669 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
671 def __init__(self, *args, **kwargs):
672 raise AttributeError(
"No constructor defined - class is abstract")
674 def read(self, filename, header, data):
675 """read(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
676 return _IMP_em2d.ImageReaderWriter_read(self, filename, header, data)
679 def read_from_floats(self, filename, header, data):
680 """read_from_floats(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
681 return _IMP_em2d.ImageReaderWriter_read_from_floats(self, filename, header, data)
684 def read_from_ints(self, filename, header, data):
685 """read_from_ints(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
686 return _IMP_em2d.ImageReaderWriter_read_from_ints(self, filename, header, data)
689 def write(self, filename, header, data):
690 """write(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
691 return _IMP_em2d.ImageReaderWriter_write(self, filename, header, data)
694 def write_to_floats(self, filename, header, data):
695 """write_to_floats(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
696 return _IMP_em2d.ImageReaderWriter_write_to_floats(self, filename, header, data)
699 def write_to_ints(self, filename, header, data):
700 """write_to_ints(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
701 return _IMP_em2d.ImageReaderWriter_write_to_ints(self, filename, header, data)
704 def get_version_info(self):
705 """get_version_info(ImageReaderWriter self) -> VersionInfo"""
706 return _IMP_em2d.ImageReaderWriter_get_version_info(self)
710 """__str__(ImageReaderWriter self) -> std::string"""
711 return _IMP_em2d.ImageReaderWriter___str__(self)
715 """__repr__(ImageReaderWriter self) -> std::string"""
716 return _IMP_em2d.ImageReaderWriter___repr__(self)
721 return _object_cast_to_ImageReaderWriter(o)
723 ImageReaderWriter_swigregister = _IMP_em2d.ImageReaderWriter_swigregister
724 ImageReaderWriter_swigregister(ImageReaderWriter)
726 class PolarResamplingParameters(object):
727 """Proxy of C++ IMP::em2d::PolarResamplingParameters class."""
729 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
731 def __init__(self, *args):
733 __init__(IMP::em2d::PolarResamplingParameters self) -> PolarResamplingParameters
734 __init__(IMP::em2d::PolarResamplingParameters self, unsigned int rows, unsigned int cols) -> PolarResamplingParameters
735 __init__(IMP::em2d::PolarResamplingParameters self, cv::Mat const & m) -> PolarResamplingParameters
737 this = _IMP_em2d.new_PolarResamplingParameters(*args)
739 self.this.append(this)
740 except __builtin__.Exception:
742 __swig_destroy__ = _IMP_em2d.delete_PolarResamplingParameters
743 __del__ =
lambda self:
None
745 def setup(self, rows, cols):
746 """setup(PolarResamplingParameters self, unsigned int rows, unsigned int cols)"""
747 return _IMP_em2d.PolarResamplingParameters_setup(self, rows, cols)
750 def get_starting_radius(self):
751 """get_starting_radius(PolarResamplingParameters self) -> double"""
752 return _IMP_em2d.PolarResamplingParameters_get_starting_radius(self)
755 def get_ending_radius(self):
756 """get_ending_radius(PolarResamplingParameters self) -> double"""
757 return _IMP_em2d.PolarResamplingParameters_get_ending_radius(self)
760 def get_radius(self, n_ring):
761 """get_radius(PolarResamplingParameters self, unsigned int n_ring) -> double"""
762 return _IMP_em2d.PolarResamplingParameters_get_radius(self, n_ring)
765 def get_number_of_rings(self):
766 """get_number_of_rings(PolarResamplingParameters self) -> unsigned int"""
767 return _IMP_em2d.PolarResamplingParameters_get_number_of_rings(self)
770 def set_estimated_number_of_angles(self, aprox_value):
771 """set_estimated_number_of_angles(PolarResamplingParameters self, unsigned int aprox_value)"""
772 return _IMP_em2d.PolarResamplingParameters_set_estimated_number_of_angles(self, aprox_value)
775 def get_number_of_angles(self):
776 """get_number_of_angles(PolarResamplingParameters self) -> unsigned int"""
777 return _IMP_em2d.PolarResamplingParameters_get_number_of_angles(self)
780 def get_angle_step(self):
781 """get_angle_step(PolarResamplingParameters self) -> double"""
782 return _IMP_em2d.PolarResamplingParameters_get_angle_step(self)
785 def get_radius_step(self):
786 """get_radius_step(PolarResamplingParameters self) -> double"""
787 return _IMP_em2d.PolarResamplingParameters_get_radius_step(self)
790 def create_maps_for_resampling(self):
791 """create_maps_for_resampling(PolarResamplingParameters self)"""
792 return _IMP_em2d.PolarResamplingParameters_create_maps_for_resampling(self)
795 def get_resampling_maps(self, m1, m2):
796 """get_resampling_maps(PolarResamplingParameters self, cv::Mat & m1, cv::Mat & m2)"""
797 return _IMP_em2d.PolarResamplingParameters_get_resampling_maps(self, m1, m2)
800 def get_resampling_map(self, m1):
801 """get_resampling_map(PolarResamplingParameters self, cv::Mat & m1)"""
802 return _IMP_em2d.PolarResamplingParameters_get_resampling_map(self, m1)
806 """show(PolarResamplingParameters self, _ostream out)"""
807 return _IMP_em2d.PolarResamplingParameters_show(self, out)
810 def get_is_setup(self):
811 """get_is_setup(PolarResamplingParameters self) -> bool"""
812 return _IMP_em2d.PolarResamplingParameters_get_is_setup(self)
816 """__str__(PolarResamplingParameters self) -> std::string"""
817 return _IMP_em2d.PolarResamplingParameters___str__(self)
821 """__repr__(PolarResamplingParameters self) -> std::string"""
822 return _IMP_em2d.PolarResamplingParameters___repr__(self)
824 PolarResamplingParameters_swigregister = _IMP_em2d.PolarResamplingParameters_swigregister
825 PolarResamplingParameters_swigregister(PolarResamplingParameters)
827 class SegmentationParameters(object):
828 """Proxy of C++ IMP::em2d::SegmentationParameters class."""
830 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
831 image_pixel_size = _swig_property(_IMP_em2d.SegmentationParameters_image_pixel_size_get, _IMP_em2d.SegmentationParameters_image_pixel_size_set)
832 diffusion_beta = _swig_property(_IMP_em2d.SegmentationParameters_diffusion_beta_get, _IMP_em2d.SegmentationParameters_diffusion_beta_set)
833 diffusion_timesteps = _swig_property(_IMP_em2d.SegmentationParameters_diffusion_timesteps_get, _IMP_em2d.SegmentationParameters_diffusion_timesteps_set)
834 fill_holes_stddevs = _swig_property(_IMP_em2d.SegmentationParameters_fill_holes_stddevs_get, _IMP_em2d.SegmentationParameters_fill_holes_stddevs_set)
835 opening_kernel = _swig_property(_IMP_em2d.SegmentationParameters_opening_kernel_get, _IMP_em2d.SegmentationParameters_opening_kernel_set)
836 remove_sizing_percentage = _swig_property(_IMP_em2d.SegmentationParameters_remove_sizing_percentage_get, _IMP_em2d.SegmentationParameters_remove_sizing_percentage_set)
837 binary_background = _swig_property(_IMP_em2d.SegmentationParameters_binary_background_get, _IMP_em2d.SegmentationParameters_binary_background_set)
838 binary_foreground = _swig_property(_IMP_em2d.SegmentationParameters_binary_foreground_get, _IMP_em2d.SegmentationParameters_binary_foreground_set)
839 threshold = _swig_property(_IMP_em2d.SegmentationParameters_threshold_get, _IMP_em2d.SegmentationParameters_threshold_set)
841 def __init__(self, *args):
843 __init__(IMP::em2d::SegmentationParameters self) -> SegmentationParameters
844 __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
846 this = _IMP_em2d.new_SegmentationParameters(*args)
848 self.this.append(this)
849 except __builtin__.Exception:
852 def show(self, *args):
854 show(SegmentationParameters self, _ostream out)
855 show(SegmentationParameters self)
857 return _IMP_em2d.SegmentationParameters_show(self, *args)
861 """__str__(SegmentationParameters self) -> std::string"""
862 return _IMP_em2d.SegmentationParameters___str__(self)
866 """__repr__(SegmentationParameters self) -> std::string"""
867 return _IMP_em2d.SegmentationParameters___repr__(self)
869 __swig_destroy__ = _IMP_em2d.delete_SegmentationParameters
870 __del__ =
lambda self:
None
871 SegmentationParameters_swigregister = _IMP_em2d.SegmentationParameters_swigregister
872 SegmentationParameters_swigregister(SegmentationParameters)
874 class MatchTemplateResult(object):
875 """Proxy of C++ IMP::em2d::MatchTemplateResult class."""
877 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
878 pair = _swig_property(_IMP_em2d.MatchTemplateResult_pair_get, _IMP_em2d.MatchTemplateResult_pair_set)
879 cross_correlation = _swig_property(_IMP_em2d.MatchTemplateResult_cross_correlation_get, _IMP_em2d.MatchTemplateResult_cross_correlation_set)
881 def __init__(self, p, cc):
882 """__init__(IMP::em2d::MatchTemplateResult self, IMP::IntPair p, double cc) -> MatchTemplateResult"""
883 this = _IMP_em2d.new_MatchTemplateResult(p, cc)
885 self.this.append(this)
886 except __builtin__.Exception:
889 def show(self, *args):
891 show(MatchTemplateResult self, _ostream out)
892 show(MatchTemplateResult self)
894 return _IMP_em2d.MatchTemplateResult_show(self, *args)
898 """__str__(MatchTemplateResult self) -> std::string"""
899 return _IMP_em2d.MatchTemplateResult___str__(self)
903 """__repr__(MatchTemplateResult self) -> std::string"""
904 return _IMP_em2d.MatchTemplateResult___repr__(self)
906 __swig_destroy__ = _IMP_em2d.delete_MatchTemplateResult
907 __del__ =
lambda self:
None
908 MatchTemplateResult_swigregister = _IMP_em2d.MatchTemplateResult_swigregister
909 MatchTemplateResult_swigregister(MatchTemplateResult)
913 """apply_mask(cv::Mat const & m, cv::Mat & result, IMP::em2d::cvIntMat const & mask, double val)"""
914 return _IMP_em2d.apply_mask(m, result, mask, val)
918 apply_circular_mask(cv::Mat const & mat, cv::Mat & result, int radius, double value=0.0)
919 apply_circular_mask(cv::Mat const & mat, cv::Mat & result, int radius)
921 return _IMP_em2d.apply_circular_mask(mat, result, radius, value)
924 """get_mean(cv::Mat const & mat, IMP::em2d::cvIntMat const & mask) -> double"""
925 return _IMP_em2d.get_mean(mat, mask)
928 """create_circular_mask(int rows, int cols, int radius) -> IMP::em2d::cvIntMat"""
929 return _IMP_em2d.create_circular_mask(rows, cols, radius)
931 def do_histogram_stretching(m, boxes, offset):
932 """do_histogram_stretching(cv::Mat & m, int boxes, int offset)"""
933 return _IMP_em2d.do_histogram_stretching(m, boxes, offset)
936 """do_dilate_and_shrink_warp(cv::Mat & m, cv::Mat const & grayscale, cv::Mat & kernel)"""
937 return _IMP_em2d.do_dilate_and_shrink_warp(m, grayscale, kernel)
941 do_morphologic_reconstruction(cv::Mat const & mask, cv::Mat & marker, int neighbors_mode=4)
942 do_morphologic_reconstruction(cv::Mat const & mask, cv::Mat & marker)
944 return _IMP_em2d.do_morphologic_reconstruction(mask, marker, neighbors_mode)
947 """do_labeling(IMP::em2d::cvIntMat const & m, IMP::em2d::cvIntMat & mat_to_label) -> int"""
948 return _IMP_em2d.do_labeling(m, mat_to_label)
951 """get_diffusion_filtering_partial_derivative(cv::Mat const & m, cv::Mat & der, double dx, double dy, double ang)"""
952 return _IMP_em2d.get_diffusion_filtering_partial_derivative(m, der, dx, dy, ang)
955 """get_domes(cv::Mat & m, cv::Mat & result, double h)"""
956 return _IMP_em2d.get_domes(m, result, h)
958 def get_transformed(input, transformed, T):
959 """get_transformed(cv::Mat const & input, cv::Mat & transformed, Transformation2D T)"""
960 return _IMP_em2d.get_transformed(input, transformed, T)
964 apply_threshold(cv::Mat & m, cv::Mat & result, double threshold=0.0)
965 apply_threshold(cv::Mat & m, cv::Mat & result)
967 return _IMP_em2d.apply_threshold(m, result, threshold)
970 """do_morphologic_contrast_enhancement(cv::Mat const & m, cv::Mat & result, cv::Mat const & kernel, unsigned int iterations)"""
971 return _IMP_em2d.do_morphologic_contrast_enhancement(m, result, kernel, iterations)
974 """get_morphologic_gradient(cv::Mat const & m, cv::Mat & result, cv::Mat const & kernel)"""
975 return _IMP_em2d.get_morphologic_gradient(m, result, kernel)
978 """get_overlap_percentage(cv::Mat & m1, cv::Mat & m2, IMP::IntPair const & center) -> double"""
979 return _IMP_em2d.get_overlap_percentage(m1, m2, center)
982 """get_best_template_matches(cv::Mat const & m, cv::Mat const & templ, unsigned int n) -> IMP::em2d::MatchTemplateResults"""
983 return _IMP_em2d.get_best_template_matches(m, templ, n)
985 """Proxy of C++ IMP::em2d::Image class."""
987 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
989 def __init__(self, *args):
991 __init__(IMP::em2d::Image self) -> Image
992 __init__(IMP::em2d::Image self, int rows, int cols) -> Image
993 __init__(IMP::em2d::Image self, IMP::String filename, ImageReaderWriter reader) -> Image
995 this = _IMP_em2d.new_Image(*args)
997 self.this.append(this)
998 except __builtin__.Exception:
1002 """get_data(Image self) -> cv::Mat &"""
1003 return _IMP_em2d.Image_get_data(self)
1006 def set_data(self, mat):
1007 """set_data(Image self, cv::Mat const & mat)"""
1008 return _IMP_em2d.Image_set_data(self, mat)
1011 def set_zeros(self):
1012 """set_zeros(Image self)"""
1013 return _IMP_em2d.Image_set_zeros(self)
1016 def set_value(self, *args):
1018 set_value(Image self, double val)
1019 set_value(Image self, int i, int j, double val)
1021 return _IMP_em2d.Image_set_value(self, *args)
1024 def __call__(self, i, j):
1025 """__call__(Image self, int i, int j) -> double"""
1026 return _IMP_em2d.Image___call__(self, i, j)
1029 def get_header(self):
1030 """get_header(Image self) -> ImageHeader"""
1031 return _IMP_em2d.Image_get_header(self)
1034 def set_size(self, *args):
1036 set_size(Image self, int rows, int cols)
1037 set_size(Image self, Image img)
1039 return _IMP_em2d.Image_set_size(self, *args)
1042 def update_header(self):
1043 """update_header(Image self)"""
1044 return _IMP_em2d.Image_update_header(self)
1047 def read(self, filename, reader):
1048 """read(Image self, IMP::String filename, ImageReaderWriter reader)"""
1049 return _IMP_em2d.Image_read(self, filename, reader)
1052 def write(self, filename, writer):
1053 """write(Image self, IMP::String const & filename, ImageReaderWriter writer)"""
1054 return _IMP_em2d.Image_write(self, filename, writer)
1057 def show(self, out):
1058 """show(Image self, _ostream out)"""
1059 return _IMP_em2d.Image_show(self, out)
1062 def get_version_info(self):
1063 """get_version_info(Image self) -> VersionInfo"""
1064 return _IMP_em2d.Image_get_version_info(self)
1067 def set_name(self, name):
1068 """set_name(Image self, IMP::String const & name)"""
1069 return _IMP_em2d.Image_set_name(self, name)
1073 """get_name(Image self) -> IMP::String"""
1074 return _IMP_em2d.Image_get_name(self)
1077 def get_min_and_max_values(self):
1078 """get_min_and_max_values(Image self) -> IMP::FloatRange"""
1079 return _IMP_em2d.Image_get_min_and_max_values(self)
1083 """__str__(Image self) -> std::string"""
1084 return _IMP_em2d.Image___str__(self)
1088 """__repr__(Image self) -> std::string"""
1089 return _IMP_em2d.Image___repr__(self)
1094 return _object_cast_to_Image(o)
1096 Image_swigregister = _IMP_em2d.Image_swigregister
1097 Image_swigregister(Image)
1101 """read_images(IMP::Strings const & names, ImageReaderWriter rw) -> IMP::em2d::Images"""
1102 return _IMP_em2d.read_images(names, rw)
1105 """save_images(IMP::em2d::Images images, IMP::Strings const & names, ImageReaderWriter rw)"""
1106 return _IMP_em2d.save_images(images, names, rw)
1110 do_normalize(cv::Mat & m)
1111 do_normalize(Image im, bool force=False)
1112 do_normalize(Image im)
1114 return _IMP_em2d.do_normalize(*args)
1118 get_histogram(cv::Mat const & m, int bins) -> IMP::Floats
1119 get_histogram(Image img, int bins) -> IMP::Floats
1121 return _IMP_em2d.get_histogram(*args)
1125 apply_variance_filter(cv::Mat const & input, cv::Mat & filtered, int kernelsize)
1126 apply_variance_filter(Image input, Image filtered, int kernelsize)
1128 return _IMP_em2d.apply_variance_filter(*args)
1132 apply_diffusion_filter(cv::Mat const & m, cv::Mat & result, double beta, double pixelsize, unsigned int time_steps)
1133 apply_diffusion_filter(Image input, Image filtered, double beta, double pixelsize, int time_steps)
1135 return _IMP_em2d.apply_diffusion_filter(*args)
1137 def do_fill_holes(*args):
1139 do_fill_holes(cv::Mat const & m, cv::Mat & result, double h)
1140 do_fill_holes(Image input, Image result, double n_stddevs)
1142 return _IMP_em2d.do_fill_holes(*args)
1144 def do_combined_fill_holes_and_threshold(*args):
1146 do_combined_fill_holes_and_threshold(cv::Mat & m, cv::Mat & result, double n_stddevs, double threshold=0.0)
1147 do_combined_fill_holes_and_threshold(cv::Mat & m, cv::Mat & result, double n_stddevs)
1148 do_combined_fill_holes_and_threshold(Image input, Image result, double n_stddevs)
1150 return _IMP_em2d.do_combined_fill_holes_and_threshold(*args)
1152 def do_extend_borders(*args):
1154 do_extend_borders(cv::Mat & orig, cv::Mat & dst, unsigned int pix)
1155 do_extend_borders(Image im1, Image im2, unsigned int pix)
1157 return _IMP_em2d.do_extend_borders(*args)
1159 def do_segmentation(*args):
1161 do_segmentation(cv::Mat const & m, cv::Mat & result, SegmentationParameters params)
1162 do_segmentation(Image input, Image result, SegmentationParameters params)
1164 return _IMP_em2d.do_segmentation(*args)
1166 def do_remove_small_objects(*args):
1168 do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage, int background=0, int foreground=1)
1169 do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage, int background=0)
1170 do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage)
1171 do_remove_small_objects(Image input, double percentage, int background=0, int foreground=1)
1172 do_remove_small_objects(Image input, double percentage, int background=0)
1173 do_remove_small_objects(Image input, double percentage)
1175 return _IMP_em2d.do_remove_small_objects(*args)
1178 """do_subtract_images(Image first, Image second, Image result)"""
1179 return _IMP_em2d.do_subtract_images(first, second, result)
1181 def add_noise(*args):
1183 add_noise(cv::Mat & v, double op1, double op2, IMP::String const & mode, double df=3)
1184 add_noise(cv::Mat & v, double op1, double op2, IMP::String const & mode)
1185 add_noise(cv::Mat & v, double op1, double op2)
1186 add_noise(Image im1, double op1, double op2, IMP::String const & mode, double df=3)
1187 add_noise(Image im1, double op1, double op2, IMP::String const & mode)
1188 add_noise(Image im1, double op1, double op2)
1190 return _IMP_em2d.add_noise(*args)
1194 do_resample_polar(cv::Mat const & input, cv::Mat & resampled, PolarResamplingParameters polar_params)
1195 do_resample_polar(Image im1, Image im2, PolarResamplingParameters polar_params)
1197 return _IMP_em2d.do_resample_polar(*args)
1201 crop(cv::Mat const & m, IMP::IntPair const & center, int size) -> cv::Mat
1202 crop(Image img, IMP::IntPair const & center, int size)
1204 return _IMP_em2d.crop(*args)
1207 """apply_mean_outside_mask(Image img, double radius)"""
1208 return _IMP_em2d.apply_mean_outside_mask(img, radius)
1209 class RegistrationResult(object):
1210 """Proxy of C++ IMP::em2d::RegistrationResult class."""
1212 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1214 def __init__(self, *args):
1216 __init__(IMP::em2d::RegistrationResult self) -> RegistrationResult
1217 __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
1218 __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0, int image_index=0) -> RegistrationResult
1219 __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0) -> RegistrationResult
1220 __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift) -> RegistrationResult
1221 __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift, int projection_index=0, int image_index=0, IMP::String name) -> RegistrationResult
1222 __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift, int projection_index=0, int image_index=0) -> RegistrationResult
1223 __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift, int projection_index=0) -> RegistrationResult
1224 __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift) -> RegistrationResult
1225 __init__(IMP::em2d::RegistrationResult self, Rotation3D R) -> RegistrationResult
1227 this = _IMP_em2d.new_RegistrationResult(*args)
1229 self.this.append(this)
1230 except __builtin__.Exception:
1234 """get_phi(RegistrationResult self) -> double"""
1235 return _IMP_em2d.RegistrationResult_get_phi(self)
1238 def get_theta(self):
1239 """get_theta(RegistrationResult self) -> double"""
1240 return _IMP_em2d.RegistrationResult_get_theta(self)
1244 """get_psi(RegistrationResult self) -> double"""
1245 return _IMP_em2d.RegistrationResult_get_psi(self)
1248 def get_shift(self):
1249 """get_shift(RegistrationResult self) -> Vector2D"""
1250 return _IMP_em2d.RegistrationResult_get_shift(self)
1253 def get_shift_3d(self):
1254 """get_shift_3d(RegistrationResult self) -> Vector3D"""
1255 return _IMP_em2d.RegistrationResult_get_shift_3d(self)
1258 def get_projection_index(self):
1259 """get_projection_index(RegistrationResult self) -> int"""
1260 return _IMP_em2d.RegistrationResult_get_projection_index(self)
1263 def set_projection_index(self, index):
1264 """set_projection_index(RegistrationResult self, int index)"""
1265 return _IMP_em2d.RegistrationResult_set_projection_index(self, index)
1268 def get_image_index(self):
1269 """get_image_index(RegistrationResult self) -> int"""
1270 return _IMP_em2d.RegistrationResult_get_image_index(self)
1273 def set_image_index(self, index):
1274 """set_image_index(RegistrationResult self, int index)"""
1275 return _IMP_em2d.RegistrationResult_set_image_index(self, index)
1279 """get_name(RegistrationResult self) -> IMP::String"""
1280 return _IMP_em2d.RegistrationResult_get_name(self)
1284 """get_ccc(RegistrationResult self) -> double"""
1285 return _IMP_em2d.RegistrationResult_get_ccc(self)
1288 def set_ccc(self, ccc):
1289 """set_ccc(RegistrationResult self, double ccc)"""
1290 return _IMP_em2d.RegistrationResult_set_ccc(self, ccc)
1293 def get_score(self):
1294 """get_score(RegistrationResult self) -> double"""
1295 return _IMP_em2d.RegistrationResult_get_score(self)
1298 def set_score(self, Score):
1299 """set_score(RegistrationResult self, double Score)"""
1300 return _IMP_em2d.RegistrationResult_set_score(self, Score)
1303 def set_rotation(self, *args):
1305 set_rotation(RegistrationResult self, double phi, double theta, double psi)
1306 set_rotation(RegistrationResult self, Rotation3D R)
1308 return _IMP_em2d.RegistrationResult_set_rotation(self, *args)
1311 def set_shift(self, shift):
1312 """set_shift(RegistrationResult self, Vector2D shift)"""
1313 return _IMP_em2d.RegistrationResult_set_shift(self, shift)
1316 def set_name(self, name):
1317 """set_name(RegistrationResult self, IMP::String name)"""
1318 return _IMP_em2d.RegistrationResult_set_name(self, name)
1321 def add_in_plane_transformation(self, t):
1322 """add_in_plane_transformation(RegistrationResult self, Transformation2D t)"""
1323 return _IMP_em2d.RegistrationResult_add_in_plane_transformation(self, t)
1326 def show(self, *args):
1328 show(RegistrationResult self, _ostream out)
1329 show(RegistrationResult self)
1331 return _IMP_em2d.RegistrationResult_show(self, *args)
1334 def write(self, *args):
1336 write(RegistrationResult self, _ostream out)
1337 write(RegistrationResult self)
1339 return _IMP_em2d.RegistrationResult_write(self, *args)
1342 def write_comment_line(self, *args):
1344 write_comment_line(RegistrationResult self, _ostream out)
1345 write_comment_line(RegistrationResult self)
1347 return _IMP_em2d.RegistrationResult_write_comment_line(self, *args)
1351 """read(RegistrationResult self, IMP::String const & s)"""
1352 return _IMP_em2d.RegistrationResult_read(self, s)
1355 def set_random_registration(self, index, maximum_shift):
1356 """set_random_registration(RegistrationResult self, unsigned int index, double maximum_shift)"""
1357 return _IMP_em2d.RegistrationResult_set_random_registration(self, index, maximum_shift)
1360 def get_rotation(self):
1361 """get_rotation(RegistrationResult self) -> Rotation3D"""
1362 return _IMP_em2d.RegistrationResult_get_rotation(self)
1365 def set_in_image(self, header):
1366 """set_in_image(RegistrationResult self, ImageHeader header)"""
1367 return _IMP_em2d.RegistrationResult_set_in_image(self, header)
1370 def read_from_image(self, header):
1371 """read_from_image(RegistrationResult self, ImageHeader header)"""
1372 return _IMP_em2d.RegistrationResult_read_from_image(self, header)
1375 def get_is_optimized_result(self):
1376 """get_is_optimized_result(RegistrationResult self) -> bool"""
1377 return _IMP_em2d.RegistrationResult_get_is_optimized_result(self)
1379 __swig_destroy__ = _IMP_em2d.delete_RegistrationResult
1380 __del__ =
lambda self:
None
1383 """__str__(RegistrationResult self) -> std::string"""
1384 return _IMP_em2d.RegistrationResult___str__(self)
1388 """__repr__(RegistrationResult self) -> std::string"""
1389 return _IMP_em2d.RegistrationResult___repr__(self)
1391 RegistrationResult_swigregister = _IMP_em2d.RegistrationResult_swigregister
1392 RegistrationResult_swigregister(RegistrationResult)
1396 """read_registration_results(IMP::String const & filename) -> IMP::em2d::RegistrationResults"""
1397 return _IMP_em2d.read_registration_results(filename)
1400 """write_registration_results(IMP::String filename, IMP::em2d::RegistrationResults const & results)"""
1401 return _IMP_em2d.write_registration_results(filename, results)
1405 get_random_registration_results(unsigned int n, double maximum_shift=5.0) -> IMP::em2d::RegistrationResults
1406 get_random_registration_results(unsigned int n) -> IMP::em2d::RegistrationResults
1408 return _IMP_em2d.get_random_registration_results(n, maximum_shift)
1411 """get_evenly_distributed_registration_results(unsigned int n_projections) -> IMP::em2d::RegistrationResults"""
1412 return _IMP_em2d.get_evenly_distributed_registration_results(n_projections)
1413 class SpiderImageReaderWriter(ImageReaderWriter):
1414 """Proxy of C++ IMP::em2d::SpiderImageReaderWriter class."""
1416 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1417 filename_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_filename__get, _IMP_em2d.SpiderImageReaderWriter_filename__set)
1418 skip_type_check_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_skip_type_check__get, _IMP_em2d.SpiderImageReaderWriter_skip_type_check__set)
1419 force_reversed_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_force_reversed__get, _IMP_em2d.SpiderImageReaderWriter_force_reversed__set)
1420 skip_extra_checkings_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__get, _IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__set)
1422 def __init__(self, *args):
1424 __init__(IMP::em2d::SpiderImageReaderWriter self) -> SpiderImageReaderWriter
1425 __init__(IMP::em2d::SpiderImageReaderWriter self, IMP::String const & filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderImageReaderWriter
1427 this = _IMP_em2d.new_SpiderImageReaderWriter(*args)
1429 self.this.append(this)
1430 except __builtin__.Exception:
1434 """__str__(SpiderImageReaderWriter self) -> std::string"""
1435 return _IMP_em2d.SpiderImageReaderWriter___str__(self)
1439 """__repr__(SpiderImageReaderWriter self) -> std::string"""
1440 return _IMP_em2d.SpiderImageReaderWriter___repr__(self)
1445 return _object_cast_to_SpiderImageReaderWriter(o)
1447 SpiderImageReaderWriter_swigregister = _IMP_em2d.SpiderImageReaderWriter_swigregister
1448 SpiderImageReaderWriter_swigregister(SpiderImageReaderWriter)
1450 class JPGImageReaderWriter(ImageReaderWriter):
1451 """Proxy of C++ IMP::em2d::JPGImageReaderWriter class."""
1453 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1456 """__init__(IMP::em2d::JPGImageReaderWriter self) -> JPGImageReaderWriter"""
1457 this = _IMP_em2d.new_JPGImageReaderWriter()
1459 self.this.append(this)
1460 except __builtin__.Exception:
1464 """__str__(JPGImageReaderWriter self) -> std::string"""
1465 return _IMP_em2d.JPGImageReaderWriter___str__(self)
1469 """__repr__(JPGImageReaderWriter self) -> std::string"""
1470 return _IMP_em2d.JPGImageReaderWriter___repr__(self)
1475 return _object_cast_to_JPGImageReaderWriter(o)
1477 JPGImageReaderWriter_swigregister = _IMP_em2d.JPGImageReaderWriter_swigregister
1478 JPGImageReaderWriter_swigregister(JPGImageReaderWriter)
1480 class TIFFImageReaderWriter(ImageReaderWriter):
1481 """Proxy of C++ IMP::em2d::TIFFImageReaderWriter class."""
1483 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1486 """__init__(IMP::em2d::TIFFImageReaderWriter self) -> TIFFImageReaderWriter"""
1487 this = _IMP_em2d.new_TIFFImageReaderWriter()
1489 self.this.append(this)
1490 except __builtin__.Exception:
1494 """__str__(TIFFImageReaderWriter self) -> std::string"""
1495 return _IMP_em2d.TIFFImageReaderWriter___str__(self)
1499 """__repr__(TIFFImageReaderWriter self) -> std::string"""
1500 return _IMP_em2d.TIFFImageReaderWriter___repr__(self)
1505 return _object_cast_to_TIFFImageReaderWriter(o)
1507 TIFFImageReaderWriter_swigregister = _IMP_em2d.TIFFImageReaderWriter_swigregister
1508 TIFFImageReaderWriter_swigregister(TIFFImageReaderWriter)
1512 """do_matrix_to_image_flip(cv::Mat & m)"""
1513 return _IMP_em2d.do_matrix_to_image_flip(m)
1516 """get_autocorrelation2d_no_preprocessing(cv::Mat const & M, cv::Mat & corr)"""
1517 return _IMP_em2d.get_autocorrelation2d_no_preprocessing(M, corr)
1521 get_autocorrelation2d(Image im1, Image im2)
1522 get_autocorrelation2d(cv::Mat const & m, cv::Mat & corr)
1524 return _IMP_em2d.get_autocorrelation2d(*args)
1528 get_correlation2d(Image im1, Image im2, Image corr)
1529 get_correlation2d(cv::Mat const & A, cv::Mat const & B, cv::Mat & corr)
1531 return _IMP_em2d.get_correlation2d(*args)
1534 """get_correlation2d_no_preprocessing(cv::Mat const & M1, cv::Mat const & M2, cv::Mat & corr)"""
1535 return _IMP_em2d.get_correlation2d_no_preprocessing(M1, M2, corr)
1538 """get_fft_using_optimal_size(cv::Mat const & m, cv::Mat & M)"""
1539 return _IMP_em2d.get_fft_using_optimal_size(m, M)
1542 """get_spectrum(cv::Mat const & m, cv::Mat & real, cv::Mat & imag)"""
1543 return _IMP_em2d.get_spectrum(m, real, imag)
1546 """get_rotation_error(RegistrationResult rr1, RegistrationResult rr2) -> double"""
1547 return _IMP_em2d.get_rotation_error(rr1, rr2)
1550 """get_shift_error(RegistrationResult rr1, RegistrationResult rr2) -> double"""
1551 return _IMP_em2d.get_shift_error(rr1, rr2)
1553 def get_average_rotation_error(correct_RRs, computed_RRs):
1554 """get_average_rotation_error(IMP::em2d::RegistrationResults const & correct_RRs, IMP::em2d::RegistrationResults const & computed_RRs) -> double"""
1555 return _IMP_em2d.get_average_rotation_error(correct_RRs, computed_RRs)
1557 def get_average_shift_error(correct_RRs, computed_RRs):
1558 """get_average_shift_error(IMP::em2d::RegistrationResults const & correct_RRs, IMP::em2d::RegistrationResults const & computed_RRs) -> double"""
1559 return _IMP_em2d.get_average_shift_error(correct_RRs, computed_RRs)
1563 get_cross_correlation_coefficient(Image im1, Image im2) -> double
1564 get_cross_correlation_coefficient(cv::Mat const & m1, cv::Mat const & m2) -> double
1566 return _IMP_em2d.get_cross_correlation_coefficient(*args)
1569 """get_global_score(IMP::em2d::RegistrationResults const & RRs) -> double"""
1570 return _IMP_em2d.get_global_score(RRs)
1572 """Proxy of C++ IMP::em2d::ScoreFunction class."""
1574 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1576 def __init__(self, *args, **kwargs):
1577 raise AttributeError(
"No constructor defined - class is abstract")
1579 def get_score(self, image, projection):
1580 """get_score(ScoreFunction self, Image image, Image projection) -> double"""
1581 return _IMP_em2d.ScoreFunction_get_score(self, image, projection)
1584 def set_variance_image(self, var):
1585 """set_variance_image(ScoreFunction self, Image var)"""
1586 return _IMP_em2d.ScoreFunction_set_variance_image(self, var)
1589 def get_version_info(self):
1590 """get_version_info(ScoreFunction self) -> VersionInfo"""
1591 return _IMP_em2d.ScoreFunction_get_version_info(self)
1595 """__str__(ScoreFunction self) -> std::string"""
1596 return _IMP_em2d.ScoreFunction___str__(self)
1600 """__repr__(ScoreFunction self) -> std::string"""
1601 return _IMP_em2d.ScoreFunction___repr__(self)
1606 return _object_cast_to_ScoreFunction(o)
1608 ScoreFunction_swigregister = _IMP_em2d.ScoreFunction_swigregister
1609 ScoreFunction_swigregister(ScoreFunction)
1611 class ChiSquaredScore(ScoreFunction):
1612 """Proxy of C++ IMP::em2d::ChiSquaredScore class."""
1614 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1617 """__init__(IMP::em2d::ChiSquaredScore self) -> ChiSquaredScore"""
1618 this = _IMP_em2d.new_ChiSquaredScore()
1620 self.this.append(this)
1621 except __builtin__.Exception:
1625 """__str__(ChiSquaredScore self) -> std::string"""
1626 return _IMP_em2d.ChiSquaredScore___str__(self)
1630 """__repr__(ChiSquaredScore self) -> std::string"""
1631 return _IMP_em2d.ChiSquaredScore___repr__(self)
1636 return _object_cast_to_ChiSquaredScore(o)
1638 __swig_destroy__ = _IMP_em2d.delete_ChiSquaredScore
1639 __del__ =
lambda self:
None
1640 ChiSquaredScore_swigregister = _IMP_em2d.ChiSquaredScore_swigregister
1641 ChiSquaredScore_swigregister(ChiSquaredScore)
1643 class EM2DScore(ScoreFunction):
1644 """Proxy of C++ IMP::em2d::EM2DScore class."""
1646 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1649 """__init__(IMP::em2d::EM2DScore self) -> EM2DScore"""
1650 this = _IMP_em2d.new_EM2DScore()
1652 self.this.append(this)
1653 except __builtin__.Exception:
1657 """__str__(EM2DScore self) -> std::string"""
1658 return _IMP_em2d.EM2DScore___str__(self)
1662 """__repr__(EM2DScore self) -> std::string"""
1663 return _IMP_em2d.EM2DScore___repr__(self)
1668 return _object_cast_to_EM2DScore(o)
1670 __swig_destroy__ = _IMP_em2d.delete_EM2DScore
1671 __del__ =
lambda self:
None
1672 EM2DScore_swigregister = _IMP_em2d.EM2DScore_swigregister
1673 EM2DScore_swigregister(EM2DScore)
1675 class MeanAbsoluteDifference(ScoreFunction):
1676 """Proxy of C++ IMP::em2d::MeanAbsoluteDifference class."""
1678 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1681 """__init__(IMP::em2d::MeanAbsoluteDifference self) -> MeanAbsoluteDifference"""
1682 this = _IMP_em2d.new_MeanAbsoluteDifference()
1684 self.this.append(this)
1685 except __builtin__.Exception:
1689 """__str__(MeanAbsoluteDifference self) -> std::string"""
1690 return _IMP_em2d.MeanAbsoluteDifference___str__(self)
1694 """__repr__(MeanAbsoluteDifference self) -> std::string"""
1695 return _IMP_em2d.MeanAbsoluteDifference___repr__(self)
1700 return _object_cast_to_MeanAbsoluteDifference(o)
1702 __swig_destroy__ = _IMP_em2d.delete_MeanAbsoluteDifference
1703 __del__ =
lambda self:
None
1704 MeanAbsoluteDifference_swigregister = _IMP_em2d.MeanAbsoluteDifference_swigregister
1705 MeanAbsoluteDifference_swigregister(MeanAbsoluteDifference)
1709 """read_selection_file(IMP::String fn) -> IMP::Strings"""
1710 return _IMP_em2d.read_selection_file(fn)
1713 """create_filenames(unsigned long number, IMP::String basic_name, IMP::String extension) -> IMP::Strings"""
1714 return _IMP_em2d.create_filenames(number, basic_name, extension)
1716 """Proxy of C++ IMP::em2d::ProjectionParameters class."""
1718 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1720 def __init__(self, *args):
1722 __init__(IMP::em2d::ProjectionParameters self) -> ProjectionParameters
1723 __init__(IMP::em2d::ProjectionParameters self, Model m, ParticleIndex id) -> ProjectionParameters
1724 __init__(IMP::em2d::ProjectionParameters self, _ParticleAdaptor d) -> ProjectionParameters
1726 this = _IMP_em2d.new_ProjectionParameters(*args)
1728 self.this.append(this)
1729 except __builtin__.Exception:
1732 def show(self, *args):
1734 show(ProjectionParameters self, _ostream out)
1735 show(ProjectionParameters self)
1737 return _IMP_em2d.ProjectionParameters_show(self, *args)
1740 def setup_particle(*args):
1742 setup_particle(Model m, ParticleIndex pi) -> ProjectionParameters
1743 setup_particle(_ParticleAdaptor decorator) -> ProjectionParameters
1745 return _IMP_em2d.ProjectionParameters_setup_particle(*args)
1747 setup_particle = staticmethod(setup_particle)
1748 __swig_destroy__ = _IMP_em2d.delete_ProjectionParameters
1749 __del__ =
lambda self:
None
1752 """get_keys() -> IMP::FloatKeys const &"""
1753 return _IMP_em2d.ProjectionParameters_get_keys()
1755 get_keys = staticmethod(get_keys)
1757 def set_proper_ranges_for_keys(self, m, min_translation_values, max_translation_values):
1758 """set_proper_ranges_for_keys(ProjectionParameters self, Model m, Vector3D min_translation_values, Vector3D max_translation_values)"""
1759 return _IMP_em2d.ProjectionParameters_set_proper_ranges_for_keys(self, m, min_translation_values, max_translation_values)
1762 def get_is_setup(*args):
1764 get_is_setup(_ParticleAdaptor p) -> bool
1765 get_is_setup(Model m, ParticleIndex pi) -> bool
1767 return _IMP_em2d.ProjectionParameters_get_is_setup(*args)
1769 get_is_setup = staticmethod(get_is_setup)
1771 def get_parameters_optimized(self):
1772 """get_parameters_optimized(ProjectionParameters self) -> bool"""
1773 return _IMP_em2d.ProjectionParameters_get_parameters_optimized(self)
1776 def get_translation(self):
1777 """get_translation(ProjectionParameters self) -> Vector3D"""
1778 return _IMP_em2d.ProjectionParameters_get_translation(self)
1781 def set_translation(self, v):
1782 """set_translation(ProjectionParameters self, Vector3D v)"""
1783 return _IMP_em2d.ProjectionParameters_set_translation(self, v)
1786 def get_rotation(self):
1787 """get_rotation(ProjectionParameters self) -> Rotation3D"""
1788 return _IMP_em2d.ProjectionParameters_get_rotation(self)
1791 def set_rotation(self, R):
1792 """set_rotation(ProjectionParameters self, Rotation3D R)"""
1793 return _IMP_em2d.ProjectionParameters_set_rotation(self, R)
1796 def set_parameters_optimized(self, tf):
1797 """set_parameters_optimized(ProjectionParameters self, bool tf)"""
1798 return _IMP_em2d.ProjectionParameters_set_parameters_optimized(self, tf)
1801 def get_quaternion_1(self):
1802 """get_quaternion_1(ProjectionParameters self) -> double"""
1803 return _IMP_em2d.ProjectionParameters_get_quaternion_1(self)
1806 def set_quaternion_1(self, t):
1807 """set_quaternion_1(ProjectionParameters self, double t)"""
1808 return _IMP_em2d.ProjectionParameters_set_quaternion_1(self, t)
1811 def get_quaternion_2(self):
1812 """get_quaternion_2(ProjectionParameters self) -> double"""
1813 return _IMP_em2d.ProjectionParameters_get_quaternion_2(self)
1816 def set_quaternion_2(self, t):
1817 """set_quaternion_2(ProjectionParameters self, double t)"""
1818 return _IMP_em2d.ProjectionParameters_set_quaternion_2(self, t)
1821 def get_quaternion_3(self):
1822 """get_quaternion_3(ProjectionParameters self) -> double"""
1823 return _IMP_em2d.ProjectionParameters_get_quaternion_3(self)
1826 def set_quaternion_3(self, t):
1827 """set_quaternion_3(ProjectionParameters self, double t)"""
1828 return _IMP_em2d.ProjectionParameters_set_quaternion_3(self, t)
1831 def get_quaternion_4(self):
1832 """get_quaternion_4(ProjectionParameters self) -> double"""
1833 return _IMP_em2d.ProjectionParameters_get_quaternion_4(self)
1836 def set_quaternion_4(self, t):
1837 """set_quaternion_4(ProjectionParameters self, double t)"""
1838 return _IMP_em2d.ProjectionParameters_set_quaternion_4(self, t)
1841 def get_translation_x(self):
1842 """get_translation_x(ProjectionParameters self) -> double"""
1843 return _IMP_em2d.ProjectionParameters_get_translation_x(self)
1846 def set_translation_x(self, t):
1847 """set_translation_x(ProjectionParameters self, double t)"""
1848 return _IMP_em2d.ProjectionParameters_set_translation_x(self, t)
1851 def get_translation_y(self):
1852 """get_translation_y(ProjectionParameters self) -> double"""
1853 return _IMP_em2d.ProjectionParameters_get_translation_y(self)
1856 def set_translation_y(self, t):
1857 """set_translation_y(ProjectionParameters self, double t)"""
1858 return _IMP_em2d.ProjectionParameters_set_translation_y(self, t)
1861 def add_attribute(self, *args):
1863 add_attribute(ProjectionParameters self, FloatKey k, IMP::Float v, bool opt)
1864 add_attribute(ProjectionParameters self, FloatKey a0, IMP::Float a1)
1865 add_attribute(ProjectionParameters self, IntKey a0, IMP::Int a1)
1866 add_attribute(ProjectionParameters self, StringKey a0, IMP::String a1)
1867 add_attribute(ProjectionParameters self, ParticleIndexKey a0, Particle a1)
1868 add_attribute(ProjectionParameters self, ObjectKey a0, Object a1)
1870 return _IMP_em2d.ProjectionParameters_add_attribute(self, *args)
1873 def get_value(self, *args):
1875 get_value(ProjectionParameters self, FloatKey a0) -> IMP::Float
1876 get_value(ProjectionParameters self, IntKey a0) -> IMP::Int
1877 get_value(ProjectionParameters self, StringKey a0) -> IMP::String
1878 get_value(ProjectionParameters self, ParticleIndexKey a0) -> Particle
1879 get_value(ProjectionParameters self, ObjectKey a0) -> Object
1881 return _IMP_em2d.ProjectionParameters_get_value(self, *args)
1884 def set_value(self, *args):
1886 set_value(ProjectionParameters self, FloatKey a0, IMP::Float a1)
1887 set_value(ProjectionParameters self, IntKey a0, IMP::Int a1)
1888 set_value(ProjectionParameters self, StringKey a0, IMP::String a1)
1889 set_value(ProjectionParameters self, ParticleIndexKey a0, Particle a1)
1890 set_value(ProjectionParameters self, ObjectKey a0, Object a1)
1892 return _IMP_em2d.ProjectionParameters_set_value(self, *args)
1895 def remove_attribute(self, *args):
1897 remove_attribute(ProjectionParameters self, FloatKey a0)
1898 remove_attribute(ProjectionParameters self, IntKey a0)
1899 remove_attribute(ProjectionParameters self, StringKey a0)
1900 remove_attribute(ProjectionParameters self, ParticleIndexKey a0)
1901 remove_attribute(ProjectionParameters self, ObjectKey a0)
1903 return _IMP_em2d.ProjectionParameters_remove_attribute(self, *args)
1906 def has_attribute(self, *args):
1908 has_attribute(ProjectionParameters self, FloatKey a0) -> bool
1909 has_attribute(ProjectionParameters self, IntKey a0) -> bool
1910 has_attribute(ProjectionParameters self, StringKey a0) -> bool
1911 has_attribute(ProjectionParameters self, ParticleIndexKey a0) -> bool
1912 has_attribute(ProjectionParameters self, ObjectKey a0) -> bool
1914 return _IMP_em2d.ProjectionParameters_has_attribute(self, *args)
1917 def get_derivative(self, a0):
1918 """get_derivative(ProjectionParameters self, FloatKey a0) -> double"""
1919 return _IMP_em2d.ProjectionParameters_get_derivative(self, a0)
1923 """get_name(ProjectionParameters self) -> std::string"""
1924 return _IMP_em2d.ProjectionParameters_get_name(self)
1927 def clear_caches(self):
1928 """clear_caches(ProjectionParameters self)"""
1929 return _IMP_em2d.ProjectionParameters_clear_caches(self)
1932 def set_name(self, a0):
1933 """set_name(ProjectionParameters self, std::string a0)"""
1934 return _IMP_em2d.ProjectionParameters_set_name(self, a0)
1938 """set_check_level(ProjectionParameters self, IMP::CheckLevel a0)"""
1939 return _IMP_em2d.ProjectionParameters_set_check_level(self, a0)
1942 def add_to_derivative(self, a0, a1, a2):
1943 """add_to_derivative(ProjectionParameters self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1944 return _IMP_em2d.ProjectionParameters_add_to_derivative(self, a0, a1, a2)
1947 def set_is_optimized(self, a0, a1):
1948 """set_is_optimized(ProjectionParameters self, FloatKey a0, bool a1)"""
1949 return _IMP_em2d.ProjectionParameters_set_is_optimized(self, a0, a1)
1952 def get_is_optimized(self, a0):
1953 """get_is_optimized(ProjectionParameters self, FloatKey a0) -> bool"""
1954 return _IMP_em2d.ProjectionParameters_get_is_optimized(self, a0)
1958 """get_check_level(ProjectionParameters self) -> IMP::CheckLevel"""
1959 return _IMP_em2d.ProjectionParameters_get_check_level(self)
1962 def __eq__(self, *args):
1964 __eq__(ProjectionParameters self, ProjectionParameters o) -> bool
1965 __eq__(ProjectionParameters self, Particle d) -> bool
1967 return _IMP_em2d.ProjectionParameters___eq__(self, *args)
1970 def __ne__(self, *args):
1972 __ne__(ProjectionParameters self, ProjectionParameters o) -> bool
1973 __ne__(ProjectionParameters self, Particle d) -> bool
1975 return _IMP_em2d.ProjectionParameters___ne__(self, *args)
1978 def __le__(self, *args):
1980 __le__(ProjectionParameters self, ProjectionParameters o) -> bool
1981 __le__(ProjectionParameters self, Particle d) -> bool
1983 return _IMP_em2d.ProjectionParameters___le__(self, *args)
1986 def __lt__(self, *args):
1988 __lt__(ProjectionParameters self, ProjectionParameters o) -> bool
1989 __lt__(ProjectionParameters self, Particle d) -> bool
1991 return _IMP_em2d.ProjectionParameters___lt__(self, *args)
1994 def __ge__(self, *args):
1996 __ge__(ProjectionParameters self, ProjectionParameters o) -> bool
1997 __ge__(ProjectionParameters self, Particle d) -> bool
1999 return _IMP_em2d.ProjectionParameters___ge__(self, *args)
2002 def __gt__(self, *args):
2004 __gt__(ProjectionParameters self, ProjectionParameters o) -> bool
2005 __gt__(ProjectionParameters self, Particle d) -> bool
2007 return _IMP_em2d.ProjectionParameters___gt__(self, *args)
2011 """__hash__(ProjectionParameters self) -> std::size_t"""
2012 return _IMP_em2d.ProjectionParameters___hash__(self)
2016 """__str__(ProjectionParameters self) -> std::string"""
2017 return _IMP_em2d.ProjectionParameters___str__(self)
2021 """__repr__(ProjectionParameters self) -> std::string"""
2022 return _IMP_em2d.ProjectionParameters___repr__(self)
2024 ProjectionParameters_swigregister = _IMP_em2d.ProjectionParameters_swigregister
2025 ProjectionParameters_swigregister(ProjectionParameters)
2027 def ProjectionParameters_setup_particle(*args):
2029 setup_particle(Model m, ParticleIndex pi) -> ProjectionParameters
2030 ProjectionParameters_setup_particle(_ParticleAdaptor decorator) -> ProjectionParameters
2032 return _IMP_em2d.ProjectionParameters_setup_particle(*args)
2034 def ProjectionParameters_get_keys():
2035 """ProjectionParameters_get_keys() -> IMP::FloatKeys const &"""
2036 return _IMP_em2d.ProjectionParameters_get_keys()
2038 def ProjectionParameters_get_is_setup(*args):
2040 get_is_setup(_ParticleAdaptor p) -> bool
2041 ProjectionParameters_get_is_setup(Model m, ParticleIndex pi) -> bool
2043 return _IMP_em2d.ProjectionParameters_get_is_setup(*args)
2046 def __lshift__(out, n):
2047 """__lshift__(_ostream out, ProjectionParameters n) -> _ostream"""
2048 return _IMP_em2d.__lshift__(out, n)
2050 """Proxy of C++ IMP::em2d::ProjectionParametersScoreState class."""
2052 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2054 def __init__(self, p):
2055 """__init__(IMP::em2d::ProjectionParametersScoreState self, Particle p) -> ProjectionParametersScoreState"""
2056 this = _IMP_em2d.new_ProjectionParametersScoreState(p)
2058 self.this.append(this)
2059 except __builtin__.Exception:
2062 def do_before_evaluate(self):
2063 """do_before_evaluate(ProjectionParametersScoreState self)"""
2064 return _IMP_em2d.ProjectionParametersScoreState_do_before_evaluate(self)
2067 def do_after_evaluate(self, da):
2068 """do_after_evaluate(ProjectionParametersScoreState self, DerivativeAccumulator da)"""
2069 return _IMP_em2d.ProjectionParametersScoreState_do_after_evaluate(self, da)
2072 def do_get_inputs(self):
2073 """do_get_inputs(ProjectionParametersScoreState self) -> IMP::ModelObjectsTemp"""
2074 return _IMP_em2d.ProjectionParametersScoreState_do_get_inputs(self)
2077 def do_get_outputs(self):
2078 """do_get_outputs(ProjectionParametersScoreState self) -> IMP::ModelObjectsTemp"""
2079 return _IMP_em2d.ProjectionParametersScoreState_do_get_outputs(self)
2082 def get_version_info(self):
2083 """get_version_info(ProjectionParametersScoreState self) -> VersionInfo"""
2084 return _IMP_em2d.ProjectionParametersScoreState_get_version_info(self)
2088 """__str__(ProjectionParametersScoreState self) -> std::string"""
2089 return _IMP_em2d.ProjectionParametersScoreState___str__(self)
2093 """__repr__(ProjectionParametersScoreState self) -> std::string"""
2094 return _IMP_em2d.ProjectionParametersScoreState___repr__(self)
2099 return _object_cast_to_ProjectionParametersScoreState(o)
2101 ProjectionParametersScoreState_swigregister = _IMP_em2d.ProjectionParametersScoreState_swigregister
2102 ProjectionParametersScoreState_swigregister(ProjectionParametersScoreState)
2104 class ProjectionMask(object):
2105 """Proxy of C++ IMP::em2d::ProjectionMask class."""
2107 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2109 def __init__(self, *args, **kwargs):
2110 raise AttributeError(
"No constructor defined")
2112 def apply(self, m, v):
2113 """apply(ProjectionMask self, cv::Mat & m, Vector2D v)"""
2114 return _IMP_em2d.ProjectionMask_apply(self, m, v)
2117 def show(self, *args):
2119 show(ProjectionMask self, _ostream out)
2120 show(ProjectionMask self)
2122 return _IMP_em2d.ProjectionMask_show(self, *args)
2124 __swig_destroy__ = _IMP_em2d.delete_ProjectionMask
2125 __del__ =
lambda self:
None
2128 """__str__(ProjectionMask self) -> std::string"""
2129 return _IMP_em2d.ProjectionMask___str__(self)
2133 """__repr__(ProjectionMask self) -> std::string"""
2134 return _IMP_em2d.ProjectionMask___repr__(self)
2136 ProjectionMask_swigregister = _IMP_em2d.ProjectionMask_swigregister
2137 ProjectionMask_swigregister(ProjectionMask)
2141 """do_place(cv::Mat & mask, cv::Mat & m, Vector2D v)"""
2142 return _IMP_em2d.do_place(mask, m, v)
2143 class MasksManager(object):
2144 """Proxy of C++ IMP::em2d::MasksManager class."""
2146 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2148 def __init__(self, *args):
2150 __init__(IMP::em2d::MasksManager self) -> MasksManager
2151 __init__(IMP::em2d::MasksManager self, double resolution, double pixelsize) -> MasksManager
2153 this = _IMP_em2d.new_MasksManager(*args)
2155 self.this.append(this)
2156 except __builtin__.Exception:
2159 def setup_kernel(self, resolution, pixelsize):
2160 """setup_kernel(MasksManager self, double resolution, double pixelsize)"""
2161 return _IMP_em2d.MasksManager_setup_kernel(self, resolution, pixelsize)
2164 def create_masks(self, ps):
2165 """create_masks(MasksManager self, IMP::ParticlesTemp const & ps)"""
2166 return _IMP_em2d.MasksManager_create_masks(self, ps)
2169 def create_mask(self, mass):
2170 """create_mask(MasksManager self, double mass)"""
2171 return _IMP_em2d.MasksManager_create_mask(self, mass)
2174 def find_mask(self, mass):
2175 """find_mask(MasksManager self, double mass) -> IMP::em2d::ProjectionMaskPtr"""
2176 return _IMP_em2d.MasksManager_find_mask(self, mass)
2179 def show(self, *args):
2181 show(MasksManager self, _ostream out)
2182 show(MasksManager self)
2184 return _IMP_em2d.MasksManager_show(self, *args)
2187 def get_number_of_masks(self):
2188 """get_number_of_masks(MasksManager self) -> unsigned int"""
2189 return _IMP_em2d.MasksManager_get_number_of_masks(self)
2191 __swig_destroy__ = _IMP_em2d.delete_MasksManager
2192 __del__ =
lambda self:
None
2195 """__str__(MasksManager self) -> std::string"""
2196 return _IMP_em2d.MasksManager___str__(self)
2200 """__repr__(MasksManager self) -> std::string"""
2201 return _IMP_em2d.MasksManager___repr__(self)
2203 MasksManager_swigregister = _IMP_em2d.MasksManager_swigregister
2204 MasksManager_swigregister(MasksManager)
2206 class ProjectingParameters(object):
2207 """Proxy of C++ IMP::em2d::ProjectingParameters class."""
2209 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2210 pixel_size = _swig_property(_IMP_em2d.ProjectingParameters_pixel_size_get, _IMP_em2d.ProjectingParameters_pixel_size_set)
2211 resolution = _swig_property(_IMP_em2d.ProjectingParameters_resolution_get, _IMP_em2d.ProjectingParameters_resolution_set)
2213 def __init__(self, *args):
2215 __init__(IMP::em2d::ProjectingParameters self) -> ProjectingParameters
2216 __init__(IMP::em2d::ProjectingParameters self, double ps, double res) -> ProjectingParameters
2218 this = _IMP_em2d.new_ProjectingParameters(*args)
2220 self.this.append(this)
2221 except __builtin__.Exception:
2224 def show(self, *args):
2226 show(ProjectingParameters self, _ostream out)
2227 show(ProjectingParameters self)
2229 return _IMP_em2d.ProjectingParameters_show(self, *args)
2233 """__str__(ProjectingParameters self) -> std::string"""
2234 return _IMP_em2d.ProjectingParameters___str__(self)
2238 """__repr__(ProjectingParameters self) -> std::string"""
2239 return _IMP_em2d.ProjectingParameters___repr__(self)
2241 __swig_destroy__ = _IMP_em2d.delete_ProjectingParameters
2242 __del__ =
lambda self:
None
2243 ProjectingParameters_swigregister = _IMP_em2d.ProjectingParameters_swigregister
2244 ProjectingParameters_swigregister(ProjectingParameters)
2246 class ProjectingOptions(ProjectingParameters):
2247 """Proxy of C++ IMP::em2d::ProjectingOptions class."""
2249 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2250 save_images = _swig_property(_IMP_em2d.ProjectingOptions_save_images_get, _IMP_em2d.ProjectingOptions_save_images_set)
2251 normalize = _swig_property(_IMP_em2d.ProjectingOptions_normalize_get, _IMP_em2d.ProjectingOptions_normalize_set)
2252 clear_matrix_before_projecting = _swig_property(_IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_get, _IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_set)
2254 def __init__(self, *args):
2256 __init__(IMP::em2d::ProjectingOptions self) -> ProjectingOptions
2257 __init__(IMP::em2d::ProjectingOptions self, double ps, double res) -> ProjectingOptions
2258 __init__(IMP::em2d::ProjectingOptions self, double ps, double res, ImageReaderWriter irw) -> ProjectingOptions
2260 this = _IMP_em2d.new_ProjectingOptions(*args)
2262 self.this.append(this)
2263 except __builtin__.Exception:
2266 def show(self, *args):
2268 show(ProjectingOptions self, _ostream out)
2269 show(ProjectingOptions self)
2271 return _IMP_em2d.ProjectingOptions_show(self, *args)
2275 """__str__(ProjectingOptions self) -> std::string"""
2276 return _IMP_em2d.ProjectingOptions___str__(self)
2280 """__repr__(ProjectingOptions self) -> std::string"""
2281 return _IMP_em2d.ProjectingOptions___repr__(self)
2283 __swig_destroy__ = _IMP_em2d.delete_ProjectingOptions
2284 __del__ =
lambda self:
None
2285 ProjectingOptions_swigregister = _IMP_em2d.ProjectingOptions_swigregister
2286 ProjectingOptions_swigregister(ProjectingOptions)
2291 get_projections(IMP::ParticlesTemp const & ps, IMP::algebra::SphericalVector3Ds const & vs, int rows, int cols, ProjectingOptions options, IMP::Strings names) -> IMP::em2d::Images
2292 get_projections(IMP::ParticlesTemp const & ps, IMP::algebra::SphericalVector3Ds const & vs, int rows, int cols, ProjectingOptions options) -> IMP::em2d::Images
2293 get_projections(IMP::ParticlesTemp const & ps, IMP::em2d::RegistrationResults const & registration_values, int rows, int cols, ProjectingOptions options, IMP::Strings names) -> IMP::em2d::Images
2294 get_projections(IMP::ParticlesTemp const & ps, IMP::em2d::RegistrationResults const & registration_values, int rows, int cols, ProjectingOptions options) -> IMP::em2d::Images
2296 return _IMP_em2d.get_projections(*args)
2300 get_projection(Image img, IMP::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks, IMP::String name)
2301 get_projection(Image img, IMP::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks)
2302 get_projection(Image img, IMP::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options)
2304 return _IMP_em2d.get_projection(*args)
2307 """do_project_particles(IMP::ParticlesTemp const & ps, cv::Mat & m2, Rotation3D R, Vector3D translation, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks)"""
2308 return _IMP_em2d.do_project_particles(ps, m2, R, translation, options, masks)
2311 """create_evenly_distributed_projections(IMP::ParticlesTemp const & ps, unsigned int n, ProjectingOptions options) -> IMP::em2d::Images"""
2312 return _IMP_em2d.create_evenly_distributed_projections(ps, n, options)
2316 do_project_vectors(IMP::algebra::Vector3Ds const & ps, Rotation3D R, Vector3D translation) -> IMP::algebra::Vector2Ds
2317 do_project_vectors(IMP::algebra::Vector3Ds const & ps, Rotation3D R, Vector3D translation, Vector3D center) -> IMP::algebra::Vector2Ds
2319 return _IMP_em2d.do_project_vectors(*args)
2322 """get_enclosing_image_size(IMP::ParticlesTemp const & ps, double pixel_size, unsigned int slack) -> unsigned int"""
2323 return _IMP_em2d.get_enclosing_image_size(ps, pixel_size, slack)
2327 get_complete_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2328 get_complete_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2330 return _IMP_em2d.get_complete_alignment(input, m_to_align, apply)
2334 get_rotational_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2335 get_rotational_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2337 return _IMP_em2d.get_rotational_alignment(input, m_to_align, apply)
2341 get_translational_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2342 get_translational_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2344 return _IMP_em2d.get_translational_alignment(input, m_to_align, apply)
2348 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
2349 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
2351 return _IMP_em2d.get_complete_alignment_no_preprocessing(input, INPUT, POLAR1, m_to_align, POLAR2, apply)
2354 """get_rotational_alignment_no_preprocessing(cv::Mat const & POLAR1, cv::Mat const & POLAR2) -> ResultAlign2D"""
2355 return _IMP_em2d.get_rotational_alignment_no_preprocessing(POLAR1, POLAR2)
2358 """get_translational_alignment_no_preprocessing(cv::Mat const & M1, cv::Mat const & M2) -> ResultAlign2D"""
2359 return _IMP_em2d.get_translational_alignment_no_preprocessing(M1, M2)
2362 """get_complete_alignment_with_centers_no_preprocessing(Vector2D center1, Vector2D center2, cv::Mat const & AUTOC_POLAR1, cv::Mat const & AUTOC_POLAR2) -> ResultAlign2D"""
2363 return _IMP_em2d.get_complete_alignment_with_centers_no_preprocessing(center1, center2, AUTOC_POLAR1, AUTOC_POLAR2)
2367 write_vectors_as_pdb(IMP::algebra::Vector2Ds const vs, IMP::String const filename)
2368 write_vectors_as_pdb(IMP::algebra::Vector3Ds const vs, IMP::String const filename)
2370 return _IMP_em2d.write_vectors_as_pdb(*args)
2371 class Em2DRestraintParameters(ProjectingParameters):
2372 """Proxy of C++ IMP::em2d::Em2DRestraintParameters class."""
2374 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2375 n_projections = _swig_property(_IMP_em2d.Em2DRestraintParameters_n_projections_get, _IMP_em2d.Em2DRestraintParameters_n_projections_set)
2376 coarse_registration_method = _swig_property(_IMP_em2d.Em2DRestraintParameters_coarse_registration_method_get, _IMP_em2d.Em2DRestraintParameters_coarse_registration_method_set)
2377 save_match_images = _swig_property(_IMP_em2d.Em2DRestraintParameters_save_match_images_get, _IMP_em2d.Em2DRestraintParameters_save_match_images_set)
2378 optimization_steps = _swig_property(_IMP_em2d.Em2DRestraintParameters_optimization_steps_get, _IMP_em2d.Em2DRestraintParameters_optimization_steps_set)
2379 simplex_initial_length = _swig_property(_IMP_em2d.Em2DRestraintParameters_simplex_initial_length_get, _IMP_em2d.Em2DRestraintParameters_simplex_initial_length_set)
2380 simplex_minimum_size = _swig_property(_IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_get, _IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_set)
2382 def __init__(self, *args):
2384 __init__(IMP::em2d::Em2DRestraintParameters self) -> Em2DRestraintParameters
2385 __init__(IMP::em2d::Em2DRestraintParameters self, double ps, double res, unsigned int n_proj=20) -> Em2DRestraintParameters
2386 __init__(IMP::em2d::Em2DRestraintParameters self, double ps, double res) -> Em2DRestraintParameters
2388 this = _IMP_em2d.new_Em2DRestraintParameters(*args)
2390 self.this.append(this)
2391 except __builtin__.Exception:
2394 def show(self, *args):
2396 show(Em2DRestraintParameters self, _ostream out)
2397 show(Em2DRestraintParameters self)
2399 return _IMP_em2d.Em2DRestraintParameters_show(self, *args)
2403 """__str__(Em2DRestraintParameters self) -> std::string"""
2404 return _IMP_em2d.Em2DRestraintParameters___str__(self)
2408 """__repr__(Em2DRestraintParameters self) -> std::string"""
2409 return _IMP_em2d.Em2DRestraintParameters___repr__(self)
2411 __swig_destroy__ = _IMP_em2d.delete_Em2DRestraintParameters
2412 __del__ =
lambda self:
None
2413 Em2DRestraintParameters_swigregister = _IMP_em2d.Em2DRestraintParameters_swigregister
2414 Em2DRestraintParameters_swigregister(Em2DRestraintParameters)
2415 cvar = _IMP_em2d.cvar
2416 ALIGN2D_NO_PREPROCESSING = cvar.ALIGN2D_NO_PREPROCESSING
2417 ALIGN2D_PREPROCESSING = cvar.ALIGN2D_PREPROCESSING
2418 ALIGN2D_WITH_CENTERS = cvar.ALIGN2D_WITH_CENTERS
2421 """Proxy of C++ IMP::em2d::ProjectionFinder class."""
2423 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2426 """__init__(IMP::em2d::ProjectionFinder self) -> ProjectionFinder"""
2427 this = _IMP_em2d.new_ProjectionFinder()
2429 self.this.append(this)
2430 except __builtin__.Exception:
2433 def setup(self, score_function, params):
2434 """setup(ProjectionFinder self, ScoreFunction score_function, Em2DRestraintParameters params)"""
2435 return _IMP_em2d.ProjectionFinder_setup(self, score_function, params)
2438 def set_subjects(self, subjects):
2439 """set_subjects(ProjectionFinder self, IMP::em2d::Images const & subjects)"""
2440 return _IMP_em2d.ProjectionFinder_set_subjects(self, subjects)
2443 def set_projections(self, projections):
2444 """set_projections(ProjectionFinder self, IMP::em2d::Images const & projections)"""
2445 return _IMP_em2d.ProjectionFinder_set_projections(self, projections)
2448 def set_variance_images(self, variances):
2449 """set_variance_images(ProjectionFinder self, IMP::em2d::Images const & variances)"""
2450 return _IMP_em2d.ProjectionFinder_set_variance_images(self, variances)
2453 def set_model_particles(self, ps):
2454 """set_model_particles(ProjectionFinder self, IMP::ParticlesTemp const & ps)"""
2455 return _IMP_em2d.ProjectionFinder_set_model_particles(self, ps)
2458 def set_save_match_images(self, x):
2459 """set_save_match_images(ProjectionFinder self, bool x)"""
2460 return _IMP_em2d.ProjectionFinder_set_save_match_images(self, x)
2463 def get_save_match_images(self):
2464 """get_save_match_images(ProjectionFinder self) -> bool"""
2465 return _IMP_em2d.ProjectionFinder_get_save_match_images(self)
2468 def set_fast_mode(self, n):
2469 """set_fast_mode(ProjectionFinder self, unsigned int n)"""
2470 return _IMP_em2d.ProjectionFinder_set_fast_mode(self, n)
2473 def get_registration_results(self):
2474 """get_registration_results(ProjectionFinder self) -> IMP::em2d::RegistrationResults"""
2475 return _IMP_em2d.ProjectionFinder_get_registration_results(self)
2478 def get_coarse_registration(self):
2479 """get_coarse_registration(ProjectionFinder self)"""
2480 return _IMP_em2d.ProjectionFinder_get_coarse_registration(self)
2483 def get_complete_registration(self):
2484 """get_complete_registration(ProjectionFinder self)"""
2485 return _IMP_em2d.ProjectionFinder_get_complete_registration(self)
2489 """get_global_score(ProjectionFinder self) -> double"""
2490 return _IMP_em2d.ProjectionFinder_get_global_score(self)
2493 def show(self, out):
2494 """show(ProjectionFinder self, _ostream out)"""
2495 return _IMP_em2d.ProjectionFinder_show(self, out)
2498 def get_preprocessing_time(self):
2499 """get_preprocessing_time(ProjectionFinder self) -> double"""
2500 return _IMP_em2d.ProjectionFinder_get_preprocessing_time(self)
2503 def get_coarse_registration_time(self):
2504 """get_coarse_registration_time(ProjectionFinder self) -> double"""
2505 return _IMP_em2d.ProjectionFinder_get_coarse_registration_time(self)
2508 def get_fine_registration_time(self):
2509 """get_fine_registration_time(ProjectionFinder self) -> double"""
2510 return _IMP_em2d.ProjectionFinder_get_fine_registration_time(self)
2513 def get_number_of_subjects(self):
2514 """get_number_of_subjects(ProjectionFinder self) -> unsigned int"""
2515 return _IMP_em2d.ProjectionFinder_get_number_of_subjects(self)
2518 def set_number_of_class_averages_members(self, n_members):
2519 """set_number_of_class_averages_members(ProjectionFinder self, IMP::Ints n_members)"""
2520 return _IMP_em2d.ProjectionFinder_set_number_of_class_averages_members(self, n_members)
2523 def get_number_of_projections(self):
2524 """get_number_of_projections(ProjectionFinder self) -> unsigned int"""
2525 return _IMP_em2d.ProjectionFinder_get_number_of_projections(self)
2528 def get_version_info(self):
2529 """get_version_info(ProjectionFinder self) -> VersionInfo"""
2530 return _IMP_em2d.ProjectionFinder_get_version_info(self)
2534 """__str__(ProjectionFinder self) -> std::string"""
2535 return _IMP_em2d.ProjectionFinder___str__(self)
2539 """__repr__(ProjectionFinder self) -> std::string"""
2540 return _IMP_em2d.ProjectionFinder___repr__(self)
2545 return _object_cast_to_ProjectionFinder(o)
2547 ProjectionFinder_swigregister = _IMP_em2d.ProjectionFinder_swigregister
2548 ProjectionFinder_swigregister(ProjectionFinder)
2551 """Proxy of C++ IMP::em2d::Em2DRestraint class."""
2553 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2555 def __init__(self, m):
2556 """__init__(IMP::em2d::Em2DRestraint self, Model m) -> Em2DRestraint"""
2557 this = _IMP_em2d.new_Em2DRestraint(m)
2559 self.this.append(this)
2560 except __builtin__.Exception:
2563 def setup(self, score_function, params):
2564 """setup(Em2DRestraint self, ScoreFunction score_function, Em2DRestraintParameters params)"""
2565 return _IMP_em2d.Em2DRestraint_setup(self, score_function, params)
2568 def set_particles(self, particles_container):
2569 """set_particles(Em2DRestraint self, SingletonContainer particles_container)"""
2570 return _IMP_em2d.Em2DRestraint_set_particles(self, particles_container)
2573 def set_images(self, em_images):
2574 """set_images(Em2DRestraint self, IMP::em2d::Images const em_images)"""
2575 return _IMP_em2d.Em2DRestraint_set_images(self, em_images)
2578 def set_variance_images(self, variance_images):
2579 """set_variance_images(Em2DRestraint self, IMP::em2d::Images const variance_images)"""
2580 return _IMP_em2d.Em2DRestraint_set_variance_images(self, variance_images)
2583 def set_fast_mode(self, n):
2584 """set_fast_mode(Em2DRestraint self, unsigned int n)"""
2585 return _IMP_em2d.Em2DRestraint_set_fast_mode(self, n)
2588 def set_coarse_registration_mode(self, opt):
2589 """set_coarse_registration_mode(Em2DRestraint self, bool opt)"""
2590 return _IMP_em2d.Em2DRestraint_set_coarse_registration_mode(self, opt)
2593 def get_registration_results(self):
2594 """get_registration_results(Em2DRestraint self) -> IMP::em2d::RegistrationResults"""
2595 return _IMP_em2d.Em2DRestraint_get_registration_results(self)
2598 def do_get_inputs(self):
2599 """do_get_inputs(Em2DRestraint self) -> IMP::ModelObjectsTemp"""
2600 return _IMP_em2d.Em2DRestraint_do_get_inputs(self)
2603 def get_version_info(self):
2604 """get_version_info(Em2DRestraint self) -> VersionInfo"""
2605 return _IMP_em2d.Em2DRestraint_get_version_info(self)
2609 """__str__(Em2DRestraint self) -> std::string"""
2610 return _IMP_em2d.Em2DRestraint___str__(self)
2614 """__repr__(Em2DRestraint self) -> std::string"""
2615 return _IMP_em2d.Em2DRestraint___repr__(self)
2620 return _object_cast_to_Em2DRestraint(o)
2622 Em2DRestraint_swigregister = _IMP_em2d.Em2DRestraint_swigregister
2623 Em2DRestraint_swigregister(Em2DRestraint)
2625 class ClusterSet(object):
2626 """Proxy of C++ IMP::em2d::ClusterSet class."""
2628 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2630 def __init__(self, N):
2631 """__init__(IMP::em2d::ClusterSet self, unsigned int N) -> ClusterSet"""
2632 this = _IMP_em2d.new_ClusterSet(N)
2634 self.this.append(this)
2635 except __builtin__.Exception:
2638 def do_join_clusters(self, cluster_id1, cluster_id2, distance_between_clusters):
2639 """do_join_clusters(ClusterSet self, unsigned int cluster_id1, unsigned int cluster_id2, double distance_between_clusters)"""
2640 return _IMP_em2d.ClusterSet_do_join_clusters(self, cluster_id1, cluster_id2, distance_between_clusters)
2643 def get_cluster_elements(self, id):
2644 """get_cluster_elements(ClusterSet self, unsigned int id) -> IMP::Ints"""
2645 return _IMP_em2d.ClusterSet_get_cluster_elements(self, id)
2648 def get_clusters_below_cutoff(self, cutoff):
2649 """get_clusters_below_cutoff(ClusterSet self, double cutoff) -> IMP::Ints"""
2650 return _IMP_em2d.ClusterSet_get_clusters_below_cutoff(self, cutoff)
2653 def get_cluster_formed_at_step(self, step):
2654 """get_cluster_formed_at_step(ClusterSet self, unsigned int step) -> IMP::Ints"""
2655 return _IMP_em2d.ClusterSet_get_cluster_formed_at_step(self, step)
2658 def get_distance_at_step(self, step):
2659 """get_distance_at_step(ClusterSet self, unsigned int step) -> double"""
2660 return _IMP_em2d.ClusterSet_get_distance_at_step(self, step)
2663 def get_id_for_cluster_at_step(self, step):
2664 """get_id_for_cluster_at_step(ClusterSet self, unsigned int step) -> unsigned int"""
2665 return _IMP_em2d.ClusterSet_get_id_for_cluster_at_step(self, step)
2668 def get_linkage_matrix(self):
2669 """get_linkage_matrix(ClusterSet self) -> IMP::FloatsList"""
2670 return _IMP_em2d.ClusterSet_get_linkage_matrix(self)
2673 def get_linkage_matrix_in_matlab_format(self):
2674 """get_linkage_matrix_in_matlab_format(ClusterSet self) -> IMP::FloatsList"""
2675 return _IMP_em2d.ClusterSet_get_linkage_matrix_in_matlab_format(self)
2678 def get_number_of_steps(self):
2679 """get_number_of_steps(ClusterSet self) -> unsigned int"""
2680 return _IMP_em2d.ClusterSet_get_number_of_steps(self)
2683 def show(self, out):
2684 """show(ClusterSet self, _ostream out)"""
2685 return _IMP_em2d.ClusterSet_show(self, out)
2689 """__str__(ClusterSet self) -> std::string"""
2690 return _IMP_em2d.ClusterSet___str__(self)
2694 """__repr__(ClusterSet self) -> std::string"""
2695 return _IMP_em2d.ClusterSet___repr__(self)
2697 __swig_destroy__ = _IMP_em2d.delete_ClusterSet
2698 __del__ =
lambda self:
None
2699 ClusterSet_swigregister = _IMP_em2d.ClusterSet_swigregister
2700 ClusterSet_swigregister(ClusterSet)
2702 class SingleLinkage(object):
2703 """Proxy of C++ IMP::em2d::SingleLinkage class."""
2705 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2708 """__init__(IMP::em2d::SingleLinkage self) -> SingleLinkage"""
2709 this = _IMP_em2d.new_SingleLinkage()
2711 self.this.append(this)
2712 except __builtin__.Exception:
2715 def __call__(self, id1, id2, cluster_set, distances):
2716 """__call__(SingleLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2717 return _IMP_em2d.SingleLinkage___call__(self, id1, id2, cluster_set, distances)
2720 def show(self, out):
2721 """show(SingleLinkage self, _ostream out)"""
2722 return _IMP_em2d.SingleLinkage_show(self, out)
2726 """__str__(SingleLinkage self) -> std::string"""
2727 return _IMP_em2d.SingleLinkage___str__(self)
2731 """__repr__(SingleLinkage self) -> std::string"""
2732 return _IMP_em2d.SingleLinkage___repr__(self)
2734 __swig_destroy__ = _IMP_em2d.delete_SingleLinkage
2735 __del__ =
lambda self:
None
2736 SingleLinkage_swigregister = _IMP_em2d.SingleLinkage_swigregister
2737 SingleLinkage_swigregister(SingleLinkage)
2739 class CompleteLinkage(object):
2740 """Proxy of C++ IMP::em2d::CompleteLinkage class."""
2742 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2745 """__init__(IMP::em2d::CompleteLinkage self) -> CompleteLinkage"""
2746 this = _IMP_em2d.new_CompleteLinkage()
2748 self.this.append(this)
2749 except __builtin__.Exception:
2752 def __call__(self, id1, id2, cluster_set, distances):
2753 """__call__(CompleteLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2754 return _IMP_em2d.CompleteLinkage___call__(self, id1, id2, cluster_set, distances)
2757 def show(self, out):
2758 """show(CompleteLinkage self, _ostream out)"""
2759 return _IMP_em2d.CompleteLinkage_show(self, out)
2763 """__str__(CompleteLinkage self) -> std::string"""
2764 return _IMP_em2d.CompleteLinkage___str__(self)
2768 """__repr__(CompleteLinkage self) -> std::string"""
2769 return _IMP_em2d.CompleteLinkage___repr__(self)
2771 __swig_destroy__ = _IMP_em2d.delete_CompleteLinkage
2772 __del__ =
lambda self:
None
2773 CompleteLinkage_swigregister = _IMP_em2d.CompleteLinkage_swigregister
2774 CompleteLinkage_swigregister(CompleteLinkage)
2776 class AverageDistanceLinkage(object):
2777 """Proxy of C++ IMP::em2d::AverageDistanceLinkage class."""
2779 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2782 """__init__(IMP::em2d::AverageDistanceLinkage self) -> AverageDistanceLinkage"""
2783 this = _IMP_em2d.new_AverageDistanceLinkage()
2785 self.this.append(this)
2786 except __builtin__.Exception:
2789 def __call__(self, id1, id2, cluster_set, distances):
2790 """__call__(AverageDistanceLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2791 return _IMP_em2d.AverageDistanceLinkage___call__(self, id1, id2, cluster_set, distances)
2794 def show(self, out):
2795 """show(AverageDistanceLinkage self, _ostream out)"""
2796 return _IMP_em2d.AverageDistanceLinkage_show(self, out)
2800 """__str__(AverageDistanceLinkage self) -> std::string"""
2801 return _IMP_em2d.AverageDistanceLinkage___str__(self)
2805 """__repr__(AverageDistanceLinkage self) -> std::string"""
2806 return _IMP_em2d.AverageDistanceLinkage___repr__(self)
2808 __swig_destroy__ = _IMP_em2d.delete_AverageDistanceLinkage
2809 __del__ =
lambda self:
None
2810 AverageDistanceLinkage_swigregister = _IMP_em2d.AverageDistanceLinkage_swigregister
2811 AverageDistanceLinkage_swigregister(AverageDistanceLinkage)
2814 """Proxy of C++ IMP::em2d::CollisionCrossSection class."""
2816 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2818 def __init__(self, n_projections, resolution, pixel_size, projection_image_size):
2819 """__init__(IMP::em2d::CollisionCrossSection self, unsigned int n_projections, double resolution, double pixel_size, double projection_image_size) -> CollisionCrossSection"""
2820 this = _IMP_em2d.new_CollisionCrossSection(n_projections, resolution, pixel_size, projection_image_size)
2822 self.this.append(this)
2823 except __builtin__.Exception:
2826 def set_model_particles(self, ps):
2827 """set_model_particles(CollisionCrossSection self, IMP::ParticlesTemp const & ps)"""
2828 return _IMP_em2d.CollisionCrossSection_set_model_particles(self, ps)
2832 """get_ccs(CollisionCrossSection self) -> double"""
2833 return _IMP_em2d.CollisionCrossSection_get_ccs(self)
2836 def show(self, out):
2837 """show(CollisionCrossSection self, _ostream out)"""
2838 return _IMP_em2d.CollisionCrossSection_show(self, out)
2841 def get_version_info(self):
2842 """get_version_info(CollisionCrossSection self) -> VersionInfo"""
2843 return _IMP_em2d.CollisionCrossSection_get_version_info(self)
2847 """__str__(CollisionCrossSection self) -> std::string"""
2848 return _IMP_em2d.CollisionCrossSection___str__(self)
2852 """__repr__(CollisionCrossSection self) -> std::string"""
2853 return _IMP_em2d.CollisionCrossSection___repr__(self)
2858 return _object_cast_to_CollisionCrossSection(o)
2860 CollisionCrossSection_swigregister = _IMP_em2d.CollisionCrossSection_swigregister
2861 CollisionCrossSection_swigregister(CollisionCrossSection)
2864 """Proxy of C++ IMP::em2d::GridStates class."""
2866 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2868 def __init__(self, *args):
2870 __init__(IMP::em2d::GridStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations, IMP::String const & name) -> GridStates
2871 __init__(IMP::em2d::GridStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations) -> GridStates
2873 this = _IMP_em2d.new_GridStates(*args)
2875 self.this.append(this)
2876 except __builtin__.Exception:
2879 def get_position(self, i):
2880 """get_position(GridStates self, unsigned int i) -> Vector3D"""
2881 return _IMP_em2d.GridStates_get_position(self, i)
2884 def get_orientation(self, i):
2885 """get_orientation(GridStates self, unsigned int i) -> Rotation3D"""
2886 return _IMP_em2d.GridStates_get_orientation(self, i)
2889 def get_version_info(self):
2890 """get_version_info(GridStates self) -> VersionInfo"""
2891 return _IMP_em2d.GridStates_get_version_info(self)
2895 """__str__(GridStates self) -> std::string"""
2896 return _IMP_em2d.GridStates___str__(self)
2900 """__repr__(GridStates self) -> std::string"""
2901 return _IMP_em2d.GridStates___repr__(self)
2906 return _object_cast_to_GridStates(o)
2908 GridStates_swigregister = _IMP_em2d.GridStates_swigregister
2909 GridStates_swigregister(GridStates)
2911 class ProjectionStates(GridStates):
2912 """Proxy of C++ IMP::em2d::ProjectionStates class."""
2914 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2916 def __init__(self, *args):
2918 __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
2919 __init__(IMP::em2d::ProjectionStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations, IMP::em2d::Images const & projections) -> ProjectionStates
2921 this = _IMP_em2d.new_ProjectionStates(*args)
2923 self.this.append(this)
2924 except __builtin__.Exception:
2928 """get_projection(ProjectionStates self, unsigned int i) -> Image"""
2929 return _IMP_em2d.ProjectionStates_get_projection(self, i)
2933 """__str__(ProjectionStates self) -> std::string"""
2934 return _IMP_em2d.ProjectionStates___str__(self)
2938 """__repr__(ProjectionStates self) -> std::string"""
2939 return _IMP_em2d.ProjectionStates___repr__(self)
2944 return _object_cast_to_ProjectionStates(o)
2946 ProjectionStates_swigregister = _IMP_em2d.ProjectionStates_swigregister
2947 ProjectionStates_swigregister(ProjectionStates)
2950 """Proxy of C++ IMP::em2d::DistanceFilter class."""
2952 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2954 def __init__(self, subset_to_act_on, subset_to_restrain, ps_table, max_distance):
2955 """__init__(IMP::em2d::DistanceFilter self, Subset subset_to_act_on, Subset subset_to_restrain, ParticleStatesTable ps_table, double max_distance) -> DistanceFilter"""
2956 this = _IMP_em2d.new_DistanceFilter(subset_to_act_on, subset_to_restrain, ps_table, max_distance)
2958 self.this.append(this)
2959 except __builtin__.Exception:
2962 def show(self, *args):
2964 show(DistanceFilter self, _ostream out)
2965 show(DistanceFilter self)
2967 return _IMP_em2d.DistanceFilter_show(self, *args)
2970 def get_version_info(self):
2971 """get_version_info(DistanceFilter self) -> VersionInfo"""
2972 return _IMP_em2d.DistanceFilter_get_version_info(self)
2976 """__str__(DistanceFilter self) -> std::string"""
2977 return _IMP_em2d.DistanceFilter___str__(self)
2981 """__repr__(DistanceFilter self) -> std::string"""
2982 return _IMP_em2d.DistanceFilter___repr__(self)
2987 return _object_cast_to_DistanceFilter(o)
2989 DistanceFilter_swigregister = _IMP_em2d.DistanceFilter_swigregister
2990 DistanceFilter_swigregister(DistanceFilter)
2993 """Proxy of C++ IMP::em2d::DistanceFilterTable class."""
2995 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2997 def __init__(self, subset_to_act_on, ps_table, max_distance):
2998 """__init__(IMP::em2d::DistanceFilterTable self, Subset subset_to_act_on, ParticleStatesTable ps_table, double max_distance) -> DistanceFilterTable"""
2999 this = _IMP_em2d.new_DistanceFilterTable(subset_to_act_on, ps_table, max_distance)
3001 self.this.append(this)
3002 except __builtin__.Exception:
3005 def show(self, *args):
3007 show(DistanceFilterTable self, _ostream out)
3008 show(DistanceFilterTable self)
3010 return _IMP_em2d.DistanceFilterTable_show(self, *args)
3013 def get_version_info(self):
3014 """get_version_info(DistanceFilterTable self) -> VersionInfo"""
3015 return _IMP_em2d.DistanceFilterTable_get_version_info(self)
3019 """__str__(DistanceFilterTable self) -> std::string"""
3020 return _IMP_em2d.DistanceFilterTable___str__(self)
3024 """__repr__(DistanceFilterTable self) -> std::string"""
3025 return _IMP_em2d.DistanceFilterTable___repr__(self)
3030 return _object_cast_to_DistanceFilterTable(o)
3032 DistanceFilterTable_swigregister = _IMP_em2d.DistanceFilterTable_swigregister
3033 DistanceFilterTable_swigregister(DistanceFilterTable)
3035 class IntsOrder(object):
3036 """Proxy of C++ IMP::em2d::IntsOrder class."""
3038 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3039 __repr__ = _swig_repr
3041 def __call__(self, a, b):
3042 """__call__(IntsOrder self, IMP::Ints const & a, IMP::Ints const & b) -> bool"""
3043 return _IMP_em2d.IntsOrder___call__(self, a, b)
3047 """__init__(IMP::em2d::IntsOrder self) -> IntsOrder"""
3048 this = _IMP_em2d.new_IntsOrder()
3050 self.this.append(this)
3051 except __builtin__.Exception:
3053 __swig_destroy__ = _IMP_em2d.delete_IntsOrder
3054 __del__ =
lambda self:
None
3055 IntsOrder_swigregister = _IMP_em2d.IntsOrder_swigregister
3056 IntsOrder_swigregister(IntsOrder)
3059 """Proxy of C++ IMP::em2d::RigidBodiesImageFitRestraint class."""
3061 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3063 def get_version_info(self):
3064 """get_version_info(RigidBodiesImageFitRestraint self) -> VersionInfo"""
3065 return _IMP_em2d.RigidBodiesImageFitRestraint_get_version_info(self)
3068 def __init__(self, scf, rbs, img):
3069 """__init__(IMP::em2d::RigidBodiesImageFitRestraint self, ScoreFunction scf, IMP::core::RigidBodies const & rbs, Image img) -> RigidBodiesImageFitRestraint"""
3070 this = _IMP_em2d.new_RigidBodiesImageFitRestraint(scf, rbs, img)
3072 self.this.append(this)
3073 except __builtin__.Exception:
3076 def set_projecting_parameters(self, p):
3077 """set_projecting_parameters(RigidBodiesImageFitRestraint self, ProjectingParameters p)"""
3078 return _IMP_em2d.RigidBodiesImageFitRestraint_set_projecting_parameters(self, p)
3081 def set_orientations(self, rb, rots):
3082 """set_orientations(RigidBodiesImageFitRestraint self, RigidBody rb, IMP::algebra::Rotation3Ds const & rots)"""
3083 return _IMP_em2d.RigidBodiesImageFitRestraint_set_orientations(self, rb, rots)
3086 def get_number_of_masks(self, rb):
3087 """get_number_of_masks(RigidBodiesImageFitRestraint self, RigidBody rb) -> unsigned int"""
3088 return _IMP_em2d.RigidBodiesImageFitRestraint_get_number_of_masks(self, rb)
3092 """__str__(RigidBodiesImageFitRestraint self) -> std::string"""
3093 return _IMP_em2d.RigidBodiesImageFitRestraint___str__(self)
3097 """__repr__(RigidBodiesImageFitRestraint self) -> std::string"""
3098 return _IMP_em2d.RigidBodiesImageFitRestraint___repr__(self)
3103 return _object_cast_to_RigidBodiesImageFitRestraint(o)
3105 RigidBodiesImageFitRestraint_swigregister = _IMP_em2d.RigidBodiesImageFitRestraint_swigregister
3106 RigidBodiesImageFitRestraint_swigregister(RigidBodiesImageFitRestraint)
3110 """get_unique_index(Rotation3D rot) -> IMP::Ints"""
3111 return _IMP_em2d.get_unique_index(rot)
3113 """Proxy of C++ IMP::em2d::RelativePositionMover class."""
3115 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3117 def __init__(self, d, max_translation, max_rotation):
3118 """__init__(IMP::em2d::RelativePositionMover self, RigidBody d, IMP::Float max_translation, IMP::Float max_rotation) -> RelativePositionMover"""
3119 this = _IMP_em2d.new_RelativePositionMover(d, max_translation, max_rotation)
3121 self.this.append(this)
3122 except __builtin__.Exception:
3125 def add_internal_transformations(self, d, transforms):
3126 """add_internal_transformations(RelativePositionMover self, RigidBody d, IMP::algebra::Transformation3Ds transforms)"""
3127 return _IMP_em2d.RelativePositionMover_add_internal_transformations(self, d, transforms)
3130 def set_random_move_probability(self, p):
3131 """set_random_move_probability(RelativePositionMover self, IMP::Float p)"""
3132 return _IMP_em2d.RelativePositionMover_set_random_move_probability(self, p)
3136 """__str__(RelativePositionMover self) -> std::string"""
3137 return _IMP_em2d.RelativePositionMover___str__(self)
3141 """__repr__(RelativePositionMover self) -> std::string"""
3142 return _IMP_em2d.RelativePositionMover___repr__(self)
3147 return _object_cast_to_RelativePositionMover(o)
3149 RelativePositionMover_swigregister = _IMP_em2d.RelativePositionMover_swigregister
3150 RelativePositionMover_swigregister(RelativePositionMover)
3153 """Proxy of C++ IMP::em2d::DummyRestraint class."""
3155 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3157 def __init__(self, p, q):
3158 """__init__(IMP::em2d::DummyRestraint self, Particle p, Particle q) -> DummyRestraint"""
3159 this = _IMP_em2d.new_DummyRestraint(p, q)
3161 self.this.append(this)
3162 except __builtin__.Exception:
3165 def show(self, *args):
3167 show(DummyRestraint self, _ostream out)
3168 show(DummyRestraint self)
3170 return _IMP_em2d.DummyRestraint_show(self, *args)
3173 def do_get_inputs(self):
3174 """do_get_inputs(DummyRestraint self) -> IMP::ModelObjectsTemp"""
3175 return _IMP_em2d.DummyRestraint_do_get_inputs(self)
3178 def get_version_info(self):
3179 """get_version_info(DummyRestraint self) -> VersionInfo"""
3180 return _IMP_em2d.DummyRestraint_get_version_info(self)
3184 """__str__(DummyRestraint self) -> std::string"""
3185 return _IMP_em2d.DummyRestraint___str__(self)
3189 """__repr__(DummyRestraint self) -> std::string"""
3190 return _IMP_em2d.DummyRestraint___repr__(self)
3195 return _object_cast_to_DummyRestraint(o)
3197 DummyRestraint_swigregister = _IMP_em2d.DummyRestraint_swigregister
3198 DummyRestraint_swigregister(DummyRestraint)
3201 """Proxy of C++ IMP::em2d::ParticlesDummyRestraint class."""
3203 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3205 def __init__(self, sc):
3206 """__init__(IMP::em2d::ParticlesDummyRestraint self, SingletonContainer sc) -> ParticlesDummyRestraint"""
3207 this = _IMP_em2d.new_ParticlesDummyRestraint(sc)
3209 self.this.append(this)
3210 except __builtin__.Exception:
3213 def show(self, *args):
3215 show(ParticlesDummyRestraint self, _ostream out)
3216 show(ParticlesDummyRestraint self)
3218 return _IMP_em2d.ParticlesDummyRestraint_show(self, *args)
3221 def do_get_inputs(self):
3222 """do_get_inputs(ParticlesDummyRestraint self) -> IMP::ModelObjectsTemp"""
3223 return _IMP_em2d.ParticlesDummyRestraint_do_get_inputs(self)
3226 def get_version_info(self):
3227 """get_version_info(ParticlesDummyRestraint self) -> VersionInfo"""
3228 return _IMP_em2d.ParticlesDummyRestraint_get_version_info(self)
3232 """__str__(ParticlesDummyRestraint self) -> std::string"""
3233 return _IMP_em2d.ParticlesDummyRestraint___str__(self)
3237 """__repr__(ParticlesDummyRestraint self) -> std::string"""
3238 return _IMP_em2d.ParticlesDummyRestraint___repr__(self)
3243 return _object_cast_to_ParticlesDummyRestraint(o)
3245 ParticlesDummyRestraint_swigregister = _IMP_em2d.ParticlesDummyRestraint_swigregister
3246 ParticlesDummyRestraint_swigregister(ParticlesDummyRestraint)
3249 """Proxy of C++ IMP::em2d::PCAFitRestraint class."""
3251 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3253 def __init__(self, particles, image_files, pixel_size, resolution=10.0, projection_number=100, reuse_direction=False, n_components=1):
3255 __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
3256 __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
3257 __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size, double resolution=10.0, unsigned int projection_number=100) -> PCAFitRestraint
3258 __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size, double resolution=10.0) -> PCAFitRestraint
3259 __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size) -> PCAFitRestraint
3261 this = _IMP_em2d.new_PCAFitRestraint(particles, image_files, pixel_size, resolution, projection_number, reuse_direction, n_components)
3263 self.this.append(this)
3264 except __builtin__.Exception:
3267 def get_projection_number(self):
3268 """get_projection_number(PCAFitRestraint self) -> unsigned int"""
3269 return _IMP_em2d.PCAFitRestraint_get_projection_number(self)
3272 def set_projection_number(self, n):
3273 """set_projection_number(PCAFitRestraint self, unsigned int n)"""
3274 return _IMP_em2d.PCAFitRestraint_set_projection_number(self, n)
3277 def write_best_projections(self, file_name, evaluate=False):
3279 write_best_projections(PCAFitRestraint self, std::string file_name, bool evaluate=False)
3280 write_best_projections(PCAFitRestraint self, std::string file_name)
3282 return _IMP_em2d.PCAFitRestraint_write_best_projections(self, file_name, evaluate)
3285 def do_get_inputs(self):
3286 """do_get_inputs(PCAFitRestraint self) -> IMP::ModelObjectsTemp"""
3287 return _IMP_em2d.PCAFitRestraint_do_get_inputs(self)
3290 def get_version_info(self):
3291 """get_version_info(PCAFitRestraint self) -> VersionInfo"""
3292 return _IMP_em2d.PCAFitRestraint_get_version_info(self)
3296 """__str__(PCAFitRestraint self) -> std::string"""
3297 return _IMP_em2d.PCAFitRestraint___str__(self)
3301 """__repr__(PCAFitRestraint self) -> std::string"""
3302 return _IMP_em2d.PCAFitRestraint___repr__(self)
3307 return _object_cast_to_PCAFitRestraint(o)
3309 PCAFitRestraint_swigregister = _IMP_em2d.PCAFitRestraint_swigregister
3310 PCAFitRestraint_swigregister(PCAFitRestraint)
3313 """Proxy of C++ std::pair<(IMP::algebra::Transformation2D,double)> class."""
3315 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3316 __repr__ = _swig_repr
3318 def __init__(self, *args):
3320 __init__(std::pair<(IMP::algebra::Transformation2D,double)> self) -> ResultAlign2D
3321 __init__(std::pair<(IMP::algebra::Transformation2D,double)> self, Transformation2D first, double second) -> ResultAlign2D
3322 __init__(std::pair<(IMP::algebra::Transformation2D,double)> self, ResultAlign2D p) -> ResultAlign2D
3324 this = _IMP_em2d.new_ResultAlign2D(*args)
3326 self.this.append(this)
3327 except __builtin__.Exception:
3329 first = _swig_property(_IMP_em2d.ResultAlign2D_first_get, _IMP_em2d.ResultAlign2D_first_set)
3330 second = _swig_property(_IMP_em2d.ResultAlign2D_second_get, _IMP_em2d.ResultAlign2D_second_set)
3334 return str((self.first, self.second))
3335 def __getitem__(self, index):
3340 def __setitem__(self, index, val):
3345 __swig_destroy__ = _IMP_em2d.delete_ResultAlign2D
3346 __del__ =
lambda self:
None
3347 ResultAlign2D_swigregister = _IMP_em2d.ResultAlign2D_swigregister
3348 ResultAlign2D_swigregister(ResultAlign2D)
3351 def _do_hierarchical_clustering_single_linkage(distances):
3352 """_do_hierarchical_clustering_single_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3353 return _IMP_em2d._do_hierarchical_clustering_single_linkage(distances)
3355 def _do_hierarchical_clustering_complete_linkage(distances):
3356 """_do_hierarchical_clustering_complete_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3357 return _IMP_em2d._do_hierarchical_clustering_complete_linkage(distances)
3359 def _do_hierarchical_clustering_average_distance_linkage(distances):
3360 """_do_hierarchical_clustering_average_distance_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3361 return _IMP_em2d._do_hierarchical_clustering_average_distance_linkage(distances)
3363 do_hierarchical_clustering_single_linkage = _do_hierarchical_clustering_single_linkage
3364 do_hierarchical_clustering_complete_linkage = _do_hierarchical_clustering_complete_linkage
3365 do_hierarchical_clustering_average_distance_linkage = _do_hierarchical_clustering_average_distance_linkage
3368 def get_module_version():
3369 """get_module_version() -> std::string const"""
3370 return _IMP_em2d.get_module_version()
3373 """get_example_path(std::string fname) -> std::string"""
3374 return _IMP_em2d.get_example_path(fname)
3377 """get_data_path(std::string fname) -> std::string"""
3378 return _IMP_em2d.get_data_path(fname)
3380 from .
import _version_check
3381 _version_check.check_version(get_module_version())
3382 __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.