Fixes to cython wrappers
Former-commit-id: 4598958f0c4bdc3262f71ce3e85467f5b07eee96
This commit is contained in:
Marek Nečada
parent
862cacf4b2
commit
833e82ab5b
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@ -6,6 +6,10 @@ import cmath
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from qpms_cdefs cimport *
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cimport cython
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from cython.parallel cimport parallel, prange
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#import enum
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# Here will be enum and dtype definitions; maybe move these to a separate file
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import math # for copysign in crep methods
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#import re # TODO for crep methods?
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@ -650,17 +654,26 @@ cdef class BaseSpec:
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def __cinit__(self, *args, **kwargs):
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cdef const qpms_uvswfi_t[:] ilist_memview
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if len(args) > 0:
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if len(args) == 0:
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if 'lMax' in kwargs.keys(): # if only lMax is specified, create the 'usual' definition in ('E','M') order
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lMax = kwargs['lMax']
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my, ny = get_mn_y(lMax)
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nelem = len(my)
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tlist = nelem * (QPMS_VSWF_ELECTRIC,) + nelem * (QPMS_VSWF_MAGNETIC,)
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mlist = 2*list(my)
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llist = 2*list(ny)
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ilist = tlm2uvswfi(tlist,llist,mlist)
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else:
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raise ValueError
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else: # len(args) > 0:
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ilist = args[0]
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#self.__ilist = np.array(args[0], dtype=qpms_uvswfi_t, order='C', copy=True) # FIXME define the dtypes at qpms_cdef.pxd level
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self.__ilist = np.array(args[0], dtype=np.ulonglong, order='C', copy=True)
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self.__ilist.setflags(write=False)
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ilist_memview = self.__ilist
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self.s.ilist = &ilist_memview[0]
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self.s.n = len(self.__ilist)
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self.s.capacity = 0 # is this the best way?
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else:
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raise ValueError
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self.__ilist = np.array(ilist, dtype=np.ulonglong, order='C', copy=True)
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self.__ilist.setflags(write=False)
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ilist_memview = self.__ilist
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self.s.ilist = &ilist_memview[0]
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self.s.n = len(self.__ilist)
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self.s.capacity = 0 # is this the best way?
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if 'norm' in kwargs.keys():
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self.s.norm = kwargs['norm']
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else:
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@ -936,7 +949,7 @@ cdef class IRot3:
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def __mul__(IRot3 self, IRot3 other):
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res = IRot3(CQuat(1,0,0,0), 1)
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res.qd = qpms_IRot3_mult(self.qd, other.qd)
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res.qd = qpms_irot3_mult(self.qd, other.qd)
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return res
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def __pow__(IRot3 self, n, _):
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@ -946,7 +959,7 @@ cdef class IRot3:
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else:
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raise ValueError("The exponent of an IRot3 has to have an integer value.")
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res = IRot3(CQuat(1,0,0,0), 1)
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res.qd = qpms_IRot3_pow(self.qd, n)
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res.qd = qpms_irot3_pow(self.qd, n)
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return res
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def isclose(IRot3 self, IRot3 other, rtol=1e-5, atol=1e-8):
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@ -1011,14 +1024,14 @@ cdef class IRot3:
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r.rot = CQuat(math.cos(math.pi/n),0,0,math.sin(math.pi/n))
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return r
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def as_uvswf_matrix(IRot3 self, basespec bspec):
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def as_uvswf_matrix(IRot3 self, BaseSpec bspec):
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'''
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Returns the uvswf representation of the current transform as a numpy array
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'''
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cdef ssize_t sz = len(bspec)
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cdef np.ndarray m = np.empty((sz, sz), dtype=complex, order='C') # FIXME explicit dtype
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cdef cdouble[:, ::1] view = m
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qpms_IRot3_uvswfi_dense(&view[0,0], bspec.rawpointer(), self.qd)
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qpms_irot3_uvswfi_dense(&view[0,0], bspec.rawpointer(), self.qd)
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return m
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cdef class TMatrixInterpolator:
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@ -1045,10 +1058,20 @@ cdef class TMatrix:
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self.t.spec = spec.rawpointer();
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# The following will raise an exception if shape is wrong
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self.m = np.array(matrix, dtype=complex, copy=True, order='C').reshape((len(spec), len(spec)))
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#self.m.setflags(write=False) # checkme
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cdef cdouble[:,::1] m_memview = self.m
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self.t.m = &(m_memview[0,0])
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self.t.owns_m = False # Memory in self.t.m is "owned" by self.m, not by self.t...
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cdef qpms_tmatrix_t *rawpointer(TMatrix self):
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'''Pointer to the qpms_tmatrix_t structure.
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Don't forget to reference the BaseSpec object itself when storing the pointer anywhere!!!
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'''
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return &(self.t)
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def as_array(TMatrix self):
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return np.array(self.m, copy=True)
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cdef class FinitePointGroup:
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'''
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Wrapper over the qpms_finite_group_t structure.
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@ -1059,7 +1082,7 @@ cdef class Particle:
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'''
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Wrapper over the qpms_particle_t structure.
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'''
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cdef readonly qpms_particle_t p
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cdef qpms_particle_t p
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cdef readonly TMatrix t # We hold the reference to the T-matrix to ensure correct reference counting
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def __cinit__(Particle self, position, TMatrix t):
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@ -1074,7 +1097,8 @@ cdef class ScatteringSystem:
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pass
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def tlm2uvswfi(t, l, m):
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''' TODO doc
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''' TODO doc
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And TODO this should rather be an ufunc.
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'''
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# Very low-priority TODO: add some types / cythonize
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if isinstance(t, int) and isinstance(l, int) and isinstance(m, int):
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@ -1082,16 +1106,19 @@ def tlm2uvswfi(t, l, m):
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elif len(t) == len(l) and len(t) == len(m):
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u = list()
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for i in range(len(t)):
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if not (isinstance(t[i], int) and isinstance(l[i], int) and isinstance(m[i], int)): # not the best check possible, though
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if not (t[i] % 1 == 0 and l[i] % 1 == 0 and m[i] % 1 == 0): # maybe not the best check possible, though
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raise ValueError # TODO error message
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u.append(qpms_tmn2uvswfi(t[i],m[i],l[i]))
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return u
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else:
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raise ValueError # TODO error message
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print(len(t), len(l), len(m))
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raise ValueError("Lengths of the t,l,m arrays must be equal, but they are %d, %d, %d."
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% (len(t), len(l), len(m)))
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def uvswfi2tlm(u):
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''' TODO doc
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and TODO this should rather be an ufunc.
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'''
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cdef qpms_vswf_type_t t
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cdef qpms_l_t l
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