switch to cpp wrapper -> first array wrapper works
This commit is contained in:
Christian Zimmermann
parent
4d2e9fc6e7
commit
c0fb3fe7ea
11 changed files with 105 additions and 464 deletions
1
.gitignore
vendored
1
.gitignore
vendored
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@ -2,4 +2,3 @@
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build/
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cnorxz.egg-info/
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*.so
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*.cpp
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@ -1,60 +0,0 @@
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from libcpp.memory cimport shared_ptr
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from range cimport cpp_RangeBase
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from index cimport cpp_YIndex
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cdef extern from "array/array.h" namespace "CNORXZ":
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cdef cppclass cpp_AIndex "CNORXZ::AIndex" [T] (cpp_YIndex):
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cpp_AIndex() except+
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cpp_AIndex(const cpp_AIndex&) except+
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cpp_AIndex(const T*, const shared_ptr[cpp_RangeBase]&, size_t lexpos) except+
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cpp_AIndex(const T*, const cpp_YIndex&) except+
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cpp_AIndex A_plus "operator+" (int n) except+
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cpp_AIndex A_minus "operator-" (int n) except+
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const T& A_get "operator*" () except+
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cdef extern from "array/array.h" namespace "CNORXZ":
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cdef cppclass cpp_BIndex "CNORXZ::BIndex" [T] (cpp_AIndex[T]):
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cpp_BIndex() except+
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cpp_BIndex(const cpp_AIndex[T]&) except+
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cpp_BIndex(const T*, const shared_ptr[cpp_RangeBase]&, size_t lexpos) except+
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cpp_BIndex(const T*, const cpp_AIndex[T]&) except+
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cpp_BIndex B_plus "operator+" (int n) except+
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cpp_BIndex B_minus "operator-" (int n) except+
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T& B_get "operator*" () except+
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cdef extern from "array/array.h" namespace "CNORXZ":
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cdef cppclass cpp_CArrayBase "CNORXZ::CArrayBase" [T]:
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cpp_CArrayBase() except+
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cpp_CArrayBase(const cpp_CArrayBase[T]&) except+
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size_t size() except+
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shared_ptr[cpp_RangeBase] range() except+
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cpp_AIndex[T] begin() except+
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cpp_AIndex[T] end() except+
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cdef extern from "array/array.h" namespace "CNORXZ":
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cdef cppclass cpp_ArrayBase "CNORXZ::ArrayBase" [T] (cpp_CArrayBase[T]):
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cpp_ArrayBase() except+
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cpp_ArrayBase(const cpp_ArrayBase[T]&) except+
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cpp_BIndex[T] begin() except+
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cpp_BIndex[T] end() except+
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cdef extern from "array/array.h" namespace "CNORXZ":
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cdef cppclass cpp_MArray "CNORXZ::MArray" [T] (cpp_ArrayBase[T]):
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cpp_MArray() except+
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cpp_MArray(const cpp_MArray[T]&) except+
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cpp_MArray(const shared_ptr[cpp_RangeBase]&) except+
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@ -1,24 +0,0 @@
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from libcpp.string cimport string
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from array cimport cpp_MArray
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cdef extern from "cereal/cnorxz_cereal.h" namespace "CNORXZ::cer":
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cdef cppclass cpp_Format "CNORXZ::cer::Format":
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pass
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cdef extern from "cereal/cnorxz_cereal.h" namespace "CNORXZ::cer::Format":
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cdef cpp_Format BINARY
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cdef cpp_Format JSON
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cdef cpp_Format XML
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cdef extern from "cereal/cnorxz_cereal.h" namespace "CNORXZ::cer":
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cdef void cpp_writeJSONFile "CNORXZ::cer::writeJSONFile" [T] (const string&, const cpp_MArray[T]&)
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cdef extern from "cereal/cnorxz_cereal.h" namespace "CNORXZ::cer":
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cdef void cpp_writeBINARYFile "CNORXZ::cer::writeBINARYFile" [T] (const string&, const cpp_MArray[T]&)
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cdef extern from "cereal/cnorxz_cereal.h" namespace "CNORXZ::cer":
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cdef void cpp_readJSONFile "CNORXZ::cer::readJSONFile" [T] (const string&, cpp_MArray[T]&)
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cdef extern from "cereal/cnorxz_cereal.h" namespace "CNORXZ::cer":
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cdef void cpp_readBINARYFile "CNORXZ::cer::readBINARYFile" [T] (const string&, cpp_MArray[T]&)
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34
cnorxz/core/core.cpp
Normal file
34
cnorxz/core/core.cpp
Normal file
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@ -0,0 +1,34 @@
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#include <Python.h>
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#include "array_wrapper.h"
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using namespace CNORXZ;
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static PyModuleDef cnorxz_core_module = {
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PyModuleDef_HEAD_INIT,
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"cnorxz",
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"cnorxz core module",
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-1,
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NULL, NULL, NULL, NULL, NULL
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};
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PyMODINIT_FUNC PyInit_cnorxz()
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{
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PyObject* m;
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PyTypeObject* carray_type = PyCArrayBType_init();
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if(carray_type == NULL){
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return NULL;
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}
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m = PyModule_Create(&cnorxz_core_module);
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if(m == NULL){
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return NULL;
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}
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Py_INCREF(carray_type);
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PyModule_AddObject(m, "CArray", (PyObject*) carray_type);
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return m;
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}
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@ -1,284 +0,0 @@
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#cython: language_level=3
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#cython: c_string_type=str
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#cython: c_string_encoding=ascii
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#cython: boundscheck=False
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#cython: wrapparound=False
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#cython: cdivision=True
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#cython: embedsignature=True
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from libcpp.memory cimport shared_ptr, make_shared, dynamic_pointer_cast
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from libcpp.string cimport string
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from libcpp cimport bool
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from cython.operator cimport dereference as deref
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from range cimport cpp_RangeBase
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from range_factory cimport cpp_RangeFactoryBase, cpp_CRangeFactory
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from array cimport cpp_CArrayBase, cpp_MArray, cpp_AIndex
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from index cimport cpp_DIndex
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from cereal cimport cpp_writeJSONFile, cpp_writeBINARYFile, cpp_readJSONFile, cpp_readBINARYFile
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## ============
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## Range
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## ============
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cdef class Range:
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cdef shared_ptr[cpp_RangeBase] cpp_range
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def size(self):
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return self.cpp_range.get().size()
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def dim(self):
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return self.cpp_range.get().dim()
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def sub(self):
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return getSubRange(self)
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def index(self):
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return getRangeIndex(self)
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cdef class RangeFactory:
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cdef shared_ptr[cpp_RangeFactoryBase] cpp_rfactory
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def __cinit__(self,rangetype,**kvargs):
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cdef size_t size = 0
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if rangetype == 'C':
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size = kvargs['size']
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self.cpp_rfactory = dynamic_pointer_cast[cpp_RangeFactoryBase,cpp_CRangeFactory](
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make_shared[cpp_CRangeFactory](size))
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else:
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raise Exception('unknown range type:'+ rangetype)
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def create(self):
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r = Range()
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r.cpp_range = self.cpp_rfactory.get().create()
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return r
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## ===========
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## Index
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## ===========
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cdef class Index:
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def __iter__(self):
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return self
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def __next__(self):
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return self
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def lex(self):
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return 0
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def dim(self):
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return 0
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def stringMeta(self):
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return ''
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cdef class DIndex (Index):
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cdef shared_ptr[cpp_DIndex] cpp_index
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cdef bool itercall
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def __cinit__(self,_range,_lexpos=0):
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cdef Range r = _range
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cdef size_t l = _lexpos
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self.cpp_index = make_shared[cpp_DIndex] (r.cpp_range,l)
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self.itercall = False
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def __iter__(self):
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self.cpp_index.get().setlpos(0)
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self.itercall = True # otherwise first (i.e. zeroth) will be excluded
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return self
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def __next__(self):
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cdef DIndex ret = self
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if self.itercall:
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ret.itercall = False
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return ret
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if self.lex() < self.cpp_index.get().range().get().size()-1:
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ret.cpp_index = make_shared[cpp_DIndex] (self.cpp_index.get().plus(1))
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return ret
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else:
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raise StopIteration
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def lex(self):
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return self.cpp_index.get().lex()
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def dim(self):
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return self.cpp_index.get().dim()
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def stringMeta(self):
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return self.cpp_index.get().stringMeta()
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def getRangeIndex(_range):
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return DIndex(_range)
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## ===========
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## Array
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## ===========
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cdef class Array:
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def size(self):
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return 0
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def range(self):
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cdef Range r = Range()
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return r
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cdef class Array_Double (Array):
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cdef shared_ptr[cpp_CArrayBase[double]] cpp_array
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def __cinit__(self,_range=None):
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cdef Range r
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if not _range is None:
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r = _range
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self.cpp_array = dynamic_pointer_cast[cpp_CArrayBase[double],cpp_MArray[double]] (make_shared[cpp_MArray[double]] (r.cpp_range) )
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def size(self):
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return self.cpp_array.get().size()
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def range(self):
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cdef Range r = Range()
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r.cpp_range = self.cpp_array.get().range()
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return r
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def index(self):
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return AIndex_Double(self)
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cdef class Array_Range (Array):
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cdef shared_ptr[cpp_CArrayBase[shared_ptr[cpp_RangeBase]]] cpp_array
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def __cinit__(self,_range=None):
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cdef Range r
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if not _range is None:
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r = _range
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self.cpp_array = dynamic_pointer_cast[cpp_CArrayBase[shared_ptr[cpp_RangeBase]],cpp_MArray[shared_ptr[cpp_RangeBase]]] (make_shared[cpp_MArray[shared_ptr[cpp_RangeBase]]] (r.cpp_range) )
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def size(self):
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return self.cpp_array.get().size()
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def range(self):
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cdef Range r = Range()
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r.cpp_range = self.cpp_array.get().range()
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return r
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def index(self):
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return AIndex_Range(self)
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def getSubRange(_range):
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cdef Range r = _range
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cdef Array_Range a = Array_Range()
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a.cpp_array = dynamic_pointer_cast[cpp_CArrayBase[shared_ptr[cpp_RangeBase]],cpp_MArray[shared_ptr[cpp_RangeBase]]] (make_shared[cpp_MArray[shared_ptr[cpp_RangeBase]]] (r.cpp_range.get().sub()) )
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return a
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def writeFile(_fname,_array,_format):
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cdef Array_Double a = _array
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cdef shared_ptr[cpp_MArray[double]] ap = dynamic_pointer_cast[cpp_MArray[double],cpp_CArrayBase[double]](a.cpp_array)
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if _format.upper() == "JSON":
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cpp_writeJSONFile[double](_fname, deref(ap.get()))
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elif _format.upper() == "BINARY":
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cpp_writeBINARYFile[double](_fname, deref(ap.get()))
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else:
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raise Exception("unknown array file format '{}'".format(_format))
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def readFile(_fname,_format):
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cdef Array_Double a = Array_Double()
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cdef shared_ptr[cpp_MArray[double]] ap = make_shared[cpp_MArray[double]]()
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a.cpp_array = dynamic_pointer_cast[cpp_CArrayBase[double],cpp_MArray[double]](ap)
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if _format.upper() == "JSON":
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cpp_readJSONFile[double](_fname, deref(ap.get()))
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elif _format.upper() == "BINARY":
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cpp_readBINARYFile[double](_fname, deref(ap.get()))
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else:
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raise Exception("unknown array file format '{}'".format(_format))
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return a
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cdef class AIndex_Double (Index):
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cdef shared_ptr[cpp_CArrayBase[double]] cpp_array # keep the instance alive
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cdef shared_ptr[cpp_AIndex[double]] cpp_index
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cdef bool itercall
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def __cinit__(self,_array,_lexpos=0):
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cdef size_t l = _lexpos
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cdef Array_Double a = _array
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self.cpp_array = a.cpp_array
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self.cpp_index = make_shared[cpp_AIndex[double]] (a.cpp_array.get().begin().A_plus(l))
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self.itercall = False
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def __iter__(self):
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self.cpp_index.get().setlpos(0)
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self.itercall = True # otherwise first (i.e. zeroth) will be excluded
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return self
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def __next__(self):
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cdef AIndex_Double ret = self
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if self.itercall:
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ret.itercall = False
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return ret
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if self.lex() < self.cpp_index.get().range().get().size()-1:
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ret.cpp_index = make_shared[cpp_AIndex[double]] (self.cpp_index.get().A_plus(1))
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return ret
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else:
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raise StopIteration
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def lex(self):
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return self.cpp_index.get().lex()
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def dim(self):
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return self.cpp_index.get().dim()
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def stringMeta(self):
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return self.cpp_index.get().stringMeta()
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def get(self):
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return self.cpp_index.get().A_get()
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cdef class AIndex_Range (Index):
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cdef shared_ptr[cpp_CArrayBase[shared_ptr[cpp_RangeBase]]] cpp_array # keep the instance alive
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cdef shared_ptr[cpp_AIndex[shared_ptr[cpp_RangeBase]]] cpp_index
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cdef bool itercall
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def __cinit__(self,_array,_lexpos=0):
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cdef size_t l = _lexpos
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cdef Array_Range a = _array
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self.cpp_array = a.cpp_array
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self.cpp_index = make_shared[cpp_AIndex[shared_ptr[cpp_RangeBase]]] (a.cpp_array.get().begin().A_plus(l))
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self.itercall = False
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def __iter__(self):
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self.cpp_index.get().setlpos(0)
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self.itercall = True # otherwise first (i.e. zeroth) will be excluded
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return self
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def __next__(self):
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cdef AIndex_Range ret = self
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if self.itercall:
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ret.itercall = False
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return ret
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if self.lex() < self.cpp_index.get().range().get().size()-1:
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ret.cpp_index = make_shared[cpp_AIndex[shared_ptr[cpp_RangeBase]]] (self.cpp_index.get().A_plus(1))
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return ret
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else:
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raise StopIteration
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def lex(self):
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return self.cpp_index.get().lex()
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def dim(self):
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return self.cpp_index.get().dim()
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def stringMeta(self):
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return self.cpp_index.get().stringMeta()
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def get(self):
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cdef Range r = Range()
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r.cpp_range = self.cpp_index.get().A_get()
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return r
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@ -1,4 +1,7 @@
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#ifndef __python_cnorxz_array_wrapper_h__
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#define __python_cnorxz_array_wrapper_h__
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#include <Python.h>
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#include "cnorxz.h"
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@ -8,7 +11,7 @@ namespace CNORXZ
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class CArrayWrapperBase
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{
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public:
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DEFAULT_MEMBERS(ArrayWrapperBase);
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DEFAULT_MEMBERS(CArrayWrapperBase);
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virtual ~CArrayWrapperBase() = default;
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virtual RangePtr range() const = 0;
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@ -23,7 +26,8 @@ namespace CNORXZ
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Sptr<CArrayBase<T>> mArr;
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public:
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DEFAULT_MEMBERS(ArrayWrapper);
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CArrayWrapper() : mArr( std::make_shared<MArray<T>>() ) {}
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//DEFAULT_MEMBERS(CArrayWrapper);
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CArrayWrapper(const RangePtr& r) : mArr( std::make_shared<MArray<T>>(r) ) {}
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virtual RangePtr range() const override final { return mArr->range(); }
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@ -37,3 +41,13 @@ struct PyCArrayB
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PyObject_HEAD
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CNORXZ::CArrayWrapperBase* ptrObj;
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};
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int PyCArrayB_init(PyCArrayB* self, PyObject* args, PyObject* kwds);
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void PyCArrayB_dealloc(PyCArrayB* self);
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PyObject* PyCArrayB_size(PyCArrayB* self);
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PyTypeObject* PyCArrayBType_init();
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extern PyMethodDef PyCArrayB_methods[];
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extern PyTypeObject PyCArrayBType;
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#endif
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@ -1,44 +0,0 @@
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from libcpp.memory cimport shared_ptr
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from libcpp.string cimport string
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from range cimport cpp_RangeBase
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|
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|
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cdef extern from "ranges/ranges.h" namespace "CNORXZ":
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cdef cppclass cpp_DIndex "CNORXZ::DIndex":
|
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cpp_DIndex() except+
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cpp_DIndex(const cpp_DIndex&) except+
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||||
cpp_DIndex(const shared_ptr[cpp_RangeBase]&, size_t lexpos) except+
|
||||
cpp_DIndex setlpos "operator=" (size_t n) except+
|
||||
cpp_DIndex setincr "operator++"() except+
|
||||
cpp_DIndex setdecr "operator--"() except+
|
||||
cpp_DIndex plus "operator+"(int n) except+
|
||||
cpp_DIndex minus "operator-"(int n) except+
|
||||
|
||||
size_t lex() except+
|
||||
size_t dim() except+
|
||||
|
||||
shared_ptr[cpp_RangeBase] range() except+
|
||||
|
||||
string stringMeta() except+
|
||||
|
||||
|
||||
cdef extern from "ranges/ranges.h" namespace "CNORXZ":
|
||||
cdef cppclass cpp_YIndex "CNORXZ::YIndex":
|
||||
cpp_YIndex() except+
|
||||
cpp_YIndex(const cpp_YIndex&) except+
|
||||
cpp_YIndex(const shared_ptr[cpp_RangeBase]&, size_t lexpos) except+
|
||||
|
||||
cpp_YIndex setlpos "operator=" (size_t n) except+
|
||||
cpp_YIndex setincr "operator++"() except+
|
||||
cpp_YIndex setdecr "operator--"() except+
|
||||
cpp_YIndex plus "operator+"(int n) except+
|
||||
cpp_YIndex minus "operator-"(int n) except+
|
||||
|
||||
size_t lex() except+
|
||||
size_t dim() except+
|
||||
|
||||
shared_ptr[cpp_RangeBase] range() except+
|
||||
|
||||
string stringMeta() except+
|
||||
|
||||
|
|
@ -1,35 +1,36 @@
|
|||
|
||||
#include "cnorxz/core/include/array_wrapper.h"
|
||||
#include "array_wrapper.h"
|
||||
|
||||
using namespace CNORXZ
|
||||
using namespace CNORXZ;
|
||||
|
||||
static int PyCArrayB_init(CArrayWrapperBase* self, PyObject* args, PyObject* kwds)
|
||||
int PyCArrayB_init(PyCArrayB* self, PyObject* args, PyObject* kwds)
|
||||
{
|
||||
static char* kwlist[] = { "type", "extension" , NULL };
|
||||
SizeT ext = 0;
|
||||
const char* type;
|
||||
|
||||
if(not PyArg_ParseTupleAndKeywords(args, kwds, "s|k", kwlist, &type, &ext)){
|
||||
return NULL;
|
||||
return -1;
|
||||
}
|
||||
|
||||
if(ext != 0){
|
||||
RangePtr r = CRangeFactory(ext).create();
|
||||
self->ptrObj = new CArrayBase<T>(r);
|
||||
// TODO: different types!!!
|
||||
self->ptrObj = new CArrayWrapper<Double>(r);
|
||||
}
|
||||
else {
|
||||
self->ptrObj = new CArrayBase<T>();
|
||||
self->ptrObj = new CArrayWrapper<Double>();
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
static void PyCArrayB_dealloc(CArrayWrapperBase* self)
|
||||
void PyCArrayB_dealloc(PyCArrayB* self)
|
||||
{
|
||||
delete self->ptrObject;
|
||||
delete self->ptrObj;
|
||||
Py_TYPE(self)->tp_free(self);
|
||||
}
|
||||
|
||||
static PyObject* PyCArrayB_size(CArrayWrapperBase* self)
|
||||
PyObject* PyCArrayB_size(PyCArrayB* self)
|
||||
{
|
||||
if(not self->ptrObj->range()){
|
||||
PyErr_SetString(PyExc_RuntimeError, "array not initialized");
|
||||
|
|
@ -39,8 +40,27 @@ static PyObject* PyCArrayB_size(CArrayWrapperBase* self)
|
|||
return Py_BuildValue("k",retval);
|
||||
}
|
||||
|
||||
static PyMethodDef PyCArrayB_methods[] = {
|
||||
{ "size", (PyCFunction)PyCArrayB_size, METH_VARARGS, "return size of the array" },
|
||||
PyMethodDef PyCArrayB_methods[] = {
|
||||
{ "size", (PyCFunction) PyCArrayB_size, METH_VARARGS, "return size of the array" },
|
||||
{ NULL }
|
||||
};
|
||||
|
||||
PyTypeObject PyCArrayBType = { PyVarObject_HEAD_INIT(NULL,0) "cnorxz.CArray" };
|
||||
|
||||
PyTypeObject* PyCArrayBType_init()
|
||||
{
|
||||
PyCArrayBType.tp_new = PyType_GenericNew;
|
||||
PyCArrayBType.tp_basicsize = sizeof(PyCArrayB);
|
||||
PyCArrayBType.tp_dealloc = (destructor) PyCArrayB_dealloc;
|
||||
PyCArrayBType.tp_flags = Py_TPFLAGS_DEFAULT;
|
||||
PyCArrayBType.tp_doc = "cnorxz CArray wrapper";
|
||||
PyCArrayBType.tp_methods = PyCArrayB_methods;
|
||||
PyCArrayBType.tp_init = (initproc) PyCArrayB_init;
|
||||
|
||||
if(PyType_Ready(&PyCArrayBType) < 0) {
|
||||
return NULL;
|
||||
}
|
||||
else {
|
||||
return &PyCArrayBType;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,11 +0,0 @@
|
|||
|
||||
from libcpp.memory cimport shared_ptr
|
||||
from array cimport cpp_MArray
|
||||
from range cimport cpp_RangeBase
|
||||
|
||||
cdef extern from "ranges/ranges.h" namespace "CNORXZ":
|
||||
cdef cppclass cpp_RangeBase "CNORXZ::RangeBase":
|
||||
size_t size() except +
|
||||
size_t dim() except +
|
||||
cpp_MArray[shared_ptr[cpp_RangeBase]] sub() except+
|
||||
|
||||
|
|
@ -1,12 +0,0 @@
|
|||
|
||||
from libcpp.memory cimport shared_ptr
|
||||
from range cimport cpp_RangeBase
|
||||
|
||||
cdef extern from "ranges/ranges.h" namespace "CNORXZ":
|
||||
cdef cppclass cpp_RangeFactoryBase "CNORXZ::RangeFactoryBase":
|
||||
shared_ptr[cpp_RangeBase] create() except +
|
||||
|
||||
cdef extern from "ranges/ranges.h" namespace "CNORXZ":
|
||||
cdef cppclass cpp_CRangeFactory "CNORXZ::CRangeFactory" (cpp_RangeFactoryBase):
|
||||
cpp_CRangeFactory(size_t size) except +
|
||||
shared_ptr[cpp_RangeBase] create() except +
|
||||
39
setup.py
39
setup.py
|
|
@ -1,7 +1,8 @@
|
|||
#!/usr/bin/env python
|
||||
|
||||
import Cython.Build
|
||||
import setuptools
|
||||
#import setuptools
|
||||
from distutils.core import setup, Extension
|
||||
import sysconfig
|
||||
import subprocess
|
||||
|
||||
|
|
@ -25,7 +26,8 @@ if git_hash_tag == git_hash and expected_cnorxz_version != cnorxz_version:
|
|||
inc_dirs = list()
|
||||
if path_to_cnorxz != "":
|
||||
inc_dirs.append( path_to_cnorxz + "/include/cnorxz" )
|
||||
|
||||
inc_dirs.append( "cnorxz/core/include" )
|
||||
|
||||
lib_dirs = list()
|
||||
lib_dirs.append( "/usr/lib" )
|
||||
lib_dirs.append( "/usr/local/lib" )
|
||||
|
|
@ -53,25 +55,32 @@ if __name__ == "__main__":
|
|||
for d in lib_dirs:
|
||||
print("\t",d)
|
||||
|
||||
extensions = list()
|
||||
extensions.append(
|
||||
setuptools.Extension(
|
||||
name = libname + ".core",
|
||||
sources = [
|
||||
"cnorxz/core/core.pyx",
|
||||
],
|
||||
define_macros=[('HAVE_CEREAL',None)],
|
||||
**default_extension_args
|
||||
)
|
||||
)
|
||||
#extensions = list()
|
||||
#extensions.append(
|
||||
# setuptools.Extension(
|
||||
# #name = libname + ".core",
|
||||
# name = libname,
|
||||
# sources = [
|
||||
# "cnorxz/core/core.cpp",
|
||||
# "cnorxz/core/lib/array_wrapper.cpp"
|
||||
# ],
|
||||
# define_macros=[('HAVE_CEREAL',None)],
|
||||
# **default_extension_args
|
||||
# )
|
||||
#)
|
||||
# append further extensions (cereal, hdf5, mpi ...) here
|
||||
|
||||
setuptools.setup(
|
||||
setup(
|
||||
name = libname,
|
||||
packages = setuptools.find_packages(),
|
||||
version = version,
|
||||
include_dirs = inc_dirs,
|
||||
ext_modules = Cython.Build.cythonize(extensions),
|
||||
ext_modules = [Extension(
|
||||
'cnorxz', ['cnorxz/core/core.cpp','cnorxz/core/lib/array_wrapper.cpp'],
|
||||
define_macros=[('HAVE_CEREAL',None)],
|
||||
**default_extension_args
|
||||
)],
|
||||
#ext_modules = Cython.Build.cythonize(extensions),
|
||||
author = author,
|
||||
author_email = author_email,
|
||||
)
|
||||
|
|
|
|||
Loading…
Reference in a new issue