more cereal wrapper + fixes

cnorxz/base/base.pyx

@@ -14,7 +14,7 @@ from range cimport cpp_RangeBase
 from range_factory cimport cpp_RangeFactoryBase, cpp_CRangeFactory
 from array cimport cpp_CArrayBase, cpp_MArray, cpp_AIndex
 from index cimport cpp_DIndex
-from cereal cimport cpp_writeJSONFile
+from cereal cimport cpp_writeJSONFile, cpp_writeBINARYFile, cpp_readJSONFile, cpp_readBINARYFile
 
 
 ## ============
@@ -133,9 +133,11 @@ cdef class Array:
 cdef class Array_Double (Array):
     cdef shared_ptr[cpp_CArrayBase[double]] cpp_array
 
-    def __cinit__(self,_range):
+    def __cinit__(self,_range=None):
-        cdef Range r = _range 
+        cdef Range r
-        self.cpp_array = dynamic_pointer_cast[cpp_CArrayBase[double],cpp_MArray[double]] (make_shared[cpp_MArray[double]] (r.cpp_range) )
+        if not _range is None:
+            r = _range
+            self.cpp_array = dynamic_pointer_cast[cpp_CArrayBase[double],cpp_MArray[double]] (make_shared[cpp_MArray[double]] (r.cpp_range) )
 
     def size(self):
         return self.cpp_array.get().size()
@@ -151,9 +153,11 @@ cdef class Array_Double (Array):
 cdef class Array_Range (Array):
     cdef shared_ptr[cpp_CArrayBase[shared_ptr[cpp_RangeBase]]] cpp_array
 
-    def __cinit__(self,_range):
+    def __cinit__(self,_range=None):
-        cdef Range r = _range 
+        cdef Range r
-        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) )
+        if not _range is None:
+            r = _range
+            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) )
 
     def size(self):
         return self.cpp_array.get().size()
@@ -162,6 +166,10 @@ cdef class Array_Range (Array):
         cdef Range r = Range()
         r.cpp_range = self.cpp_array.get().range()
         return r
+
+    def index(self):
+        return AIndex_Range(self)
+
     
 def getSubRange(_range):
     cdef Range r = _range
@@ -169,19 +177,38 @@ def getSubRange(_range):
     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()) )
     return a
 
-def writeJSONFile(_fname,_array):
+def writeFile(_fname,_array,_format):
     cdef Array_Double a = _array
     cdef shared_ptr[cpp_MArray[double]] ap = dynamic_pointer_cast[cpp_MArray[double],cpp_CArrayBase[double]](a.cpp_array)
-    cpp_writeJSONFile[double](_fname, deref(ap.get()))
+    if _format.upper() == "JSON":
+        cpp_writeJSONFile[double](_fname, deref(ap.get()))
+    elif _format.upper() == "BINARY":
+        cpp_writeBINARYFile[double](_fname, deref(ap.get()))
+    else:
+        raise Exception("unknown array file format '{}'".format(_format))
+
+def readFile(_fname,_format):
+    cdef Array_Double a = Array_Double()
+    cdef shared_ptr[cpp_MArray[double]] ap = make_shared[cpp_MArray[double]]()
+    a.cpp_array = dynamic_pointer_cast[cpp_CArrayBase[double],cpp_MArray[double]](ap)
+    if _format.upper() == "JSON":
+        cpp_readJSONFile[double](_fname, deref(ap.get()))
+    elif _format.upper() == "BINARY":
+        cpp_readBINARYFile[double](_fname, deref(ap.get()))
+    else:
+        raise Exception("unknown array file format '{}'".format(_format))
+    return a
 
 
 cdef class AIndex_Double (Index):
+    cdef shared_ptr[cpp_CArrayBase[double]] cpp_array # keep the instance alive
     cdef shared_ptr[cpp_AIndex[double]] cpp_index
     cdef bool itercall
 
     def __cinit__(self,_array,_lexpos=0):
         cdef size_t l = _lexpos
         cdef Array_Double a = _array
+        self.cpp_array = a.cpp_array
         self.cpp_index = make_shared[cpp_AIndex[double]] (a.cpp_array.get().begin().A_plus(l))
         self.itercall = False
 
@@ -212,3 +239,46 @@ cdef class AIndex_Double (Index):
     
     def get(self):
         return self.cpp_index.get().A_get()
+
+    
+cdef class AIndex_Range (Index):
+    cdef shared_ptr[cpp_CArrayBase[shared_ptr[cpp_RangeBase]]] cpp_array # keep the instance alive
+    cdef shared_ptr[cpp_AIndex[shared_ptr[cpp_RangeBase]]] cpp_index
+    cdef bool itercall
+
+    def __cinit__(self,_array,_lexpos=0):
+        cdef size_t l = _lexpos
+        cdef Array_Range a = _array
+        self.cpp_array = a.cpp_array
+        self.cpp_index = make_shared[cpp_AIndex[shared_ptr[cpp_RangeBase]]] (a.cpp_array.get().begin().A_plus(l))
+        self.itercall = False
+
+    def __iter__(self):
+        self.cpp_index.get().setlpos(0)
+        self.itercall = True # otherwise first (i.e. zeroth) will be excluded
+        return self
+
+    def __next__(self):
+        cdef AIndex_Range ret = self
+        if self.itercall:
+            ret.itercall = False
+            return ret
+        if self.lex() < self.cpp_index.get().range().get().size()-1:
+            ret.cpp_index = make_shared[cpp_AIndex[shared_ptr[cpp_RangeBase]]] (self.cpp_index.get().A_plus(1))
+            return ret
+        else:
+            raise StopIteration
+
+    def lex(self):
+        return self.cpp_index.get().lex()
+
+    def dim(self):
+        return self.cpp_index.get().dim()
+
+    def stringMeta(self):
+        return self.cpp_index.get().stringMeta()
+    
+    def get(self):
+        cdef Range r = Range()
+        r.cpp_range = self.cpp_index.get().A_get()
+        return r

cnorxz/base/cereal.pxd

@@ -13,3 +13,12 @@ cdef extern from "cereal/cnorxz_cereal.h" namespace "CNORXZ::cer::Format":
 
 cdef extern from "cereal/cnorxz_cereal.h" namespace "CNORXZ::cer":
     cdef void cpp_writeJSONFile "CNORXZ::cer::writeJSONFile" [T] (const string&, const cpp_MArray[T]&)
+
+cdef extern from "cereal/cnorxz_cereal.h" namespace "CNORXZ::cer":
+    cdef void cpp_writeBINARYFile "CNORXZ::cer::writeBINARYFile" [T] (const string&, const cpp_MArray[T]&)
+
+cdef extern from "cereal/cnorxz_cereal.h" namespace "CNORXZ::cer":
+    cdef void cpp_readJSONFile "CNORXZ::cer::readJSONFile" [T] (const string&, cpp_MArray[T]&)
+
+cdef extern from "cereal/cnorxz_cereal.h" namespace "CNORXZ::cer":
+    cdef void cpp_readBINARYFile "CNORXZ::cer::readBINARYFile" [T] (const string&, cpp_MArray[T]&)