From 564b3eebb5c4cd346cca496a7f5d5f8fa19bbca0 Mon Sep 17 00:00:00 2001
From: Christian Zimmermann <christian.zimmermann@ur.de>
Date: Tue, 6 Feb 2024 01:41:49 +0100
Subject: [PATCH] WIP...
---
cnorxz/core/include/array_wrapper.h | 59 +++++++++++++++-
cnorxz/core/lib/array_wrapper.cpp | 101 ++++++++++++++++++++++++++--
cnorxz/core/lib/range_wrapper.cpp | 2 +
setup.py | 7 +-
4 files changed, 160 insertions(+), 9 deletions(-)
diff --git a/cnorxz/core/include/array_wrapper.h b/cnorxz/core/include/array_wrapper.h
index fb553fc..a13ee9f 100644
--- a/cnorxz/core/include/array_wrapper.h
+++ b/cnorxz/core/include/array_wrapper.h
@@ -4,6 +4,8 @@
#include <Python.h>
#include "cnorxz.h"
+#include "cereal/cnorxz_cereal.h"
+#include "numpy/ndarraytypes.h"
namespace CNORXZ
{
@@ -18,9 +20,42 @@ namespace CNORXZ
virtual SizeT size() const = 0;
// virtual PyObject* get() const = 0; // operator[]!!
#ifdef HAVE_CEREAL
- virtual void writeFile(Format f, const String& fname);
- virtual void readFile(Format f, const String& fname);
+ virtual void writeFile(cer::Format f, const String& fname) const = 0;
+ virtual void readFile(cer::Format f, const String& fname) const = 0;
#endif
+ virtual int typenum() const = 0;
+ virtual const void* data() const = 0;
+ virtual SizeT datasize() const = 0;
+ };
+
+ template <typename T>
+ struct Typenum
+ {
+ static const int value = NPY_NOTYPE;
+ };
+
+ template <>
+ struct Typenum<Double>
+ {
+ static const int value = NPY_DOUBLE;
+ };
+
+ template <>
+ struct Typenum<Int>
+ {
+ static const int value = NPY_INT32;
+ };
+
+ template <>
+ struct Typenum<LInt>
+ {
+ static const int value = NPY_INT64;
+ };
+
+ template <>
+ struct Typenum<SizeT>
+ {
+ static const int value = NPY_UINT64;
};
template <typename T>
@@ -31,11 +66,29 @@ namespace CNORXZ
public:
CArrayWrapper() : mArr( std::make_shared<MArray<T>>() ) {}
- //DEFAULT_MEMBERS(CArrayWrapper);
CArrayWrapper(const RangePtr& r) : mArr( std::make_shared<MArray<T>>(r) ) {}
virtual RangePtr range() const override final { return mArr->range(); }
virtual SizeT size() const override final { return mArr->size(); }
+#ifdef HAVE_CEREAL
+ virtual void writeFile(cer::Format f, const String& fname) const override final
+ {
+ if(f == cer::Format::XML) { cer::writeXMLFile(fname, *mArr); }
+ else if(f == cer::Format::JSON) { cer::writeJSONFile(fname, *mArr); }
+ else { cer::writeBINARYFile(fname, *mArr); }
+ }
+
+ virtual void readFile(cer::Format f, const String& fname) const override final
+ {
+ if(f == cer::Format::XML) { cer::readXMLFile(fname, *mArr); }
+ else if(f == cer::Format::JSON) { cer::readJSONFile(fname, *mArr); }
+ else { cer::readBINARYFile(fname, *mArr); }
+ }
+#endif
+ virtual int typenum() const override final { return Typenum<T>::value; }
+ virtual const void* data() const override final
+ { return reinterpret_cast<const void*>( mArr->data() ); }
+ virtual SizeT datasize() const override final { return size() * sizeof(T); }
};
}
diff --git a/cnorxz/core/lib/array_wrapper.cpp b/cnorxz/core/lib/array_wrapper.cpp
index c7ba2b1..5957a44 100644
--- a/cnorxz/core/lib/array_wrapper.cpp
+++ b/cnorxz/core/lib/array_wrapper.cpp
@@ -1,13 +1,15 @@
#include "array_wrapper.h"
+#include "numpy/arrayobject.h"
using namespace CNORXZ;
+using namespace CNORXZ::cer;
int PyCArrayB_init(PyCArrayB* self, PyObject* args, PyObject* kwds)
{
static char* kwlist[] = { "type", "extension" , NULL };
SizeT ext = 0;
- const char* type;
+ char* type = NULL;
if(not PyArg_ParseTupleAndKeywords(args, kwds, "s|k", kwlist, &type, &ext)){
return -1;
@@ -37,12 +39,103 @@ PyObject* PyCArrayB_size(PyCArrayB* self)
return NULL;
}
const SizeT retval = self->ptrObj->size();
- return Py_BuildValue("k",retval);
+ return Py_BuildValue("k", retval);
+}
+
+PyObject* PyCArrayB_range(PyCArrayB* self)
+{
+ if(not self->ptrObj->range()){
+ PyErr_SetString(PyExc_RuntimeError, "array not initialized");
+ return NULL;
+ }
+ const RangePtr retval = self->ptrObj->range();
+ return Py_BuildValue("k", retval);
+}
+
+Format formatFromString(const char* fstr)
+{
+ Format f = Format::BINARY;
+ if(fstr != NULL){
+ if(strcmp(fstr,"binary") == 0){
+ f = Format::BINARY;
+ }
+ else if(strcmp(fstr,"json") == 0){
+ f = Format::JSON;
+ }
+ else if(strcmp(fstr,"xml") == 0){
+ f = Format::XML;
+ }
+ else {
+ PyErr_SetString(PyExc_RuntimeError, "unknown format");
+ }
+ }
+ return f;
+}
+
+void PyCArrayB_writeFile(PyCArrayB* self, PyObject* args, PyObject* kwds)
+{
+ if(not self->ptrObj->range()){
+ PyErr_SetString(PyExc_RuntimeError, "array not initialized");
+ }
+ static char* kwlist[] = { "format", "filename" , NULL };
+ char* fname = NULL;
+ char* format = NULL;
+
+ if(not PyArg_ParseTupleAndKeywords(args, kwds, "s|s", kwlist, &fname, &format)){
+ return;
+ }
+ const String fn(fname);
+ const Format f = formatFromString(format);
+ self->ptrObj->writeFile(f, fn);
+}
+
+void PyCArrayB_readFile(PyCArrayB* self, PyObject* args, PyObject* kwds)
+{
+ static char* kwlist[] = { "format", "filename" , NULL };
+ char* fname = NULL;
+ char* format = NULL;
+
+ if(not PyArg_ParseTupleAndKeywords(args, kwds, "s|s", kwlist, &fname, &format)){
+ return;
+ }
+ const String fn(fname);
+ const Format f = formatFromString(format);
+ self->ptrObj->readFile(f, fn);
+}
+
+PyObject* PyCArrayB_npa(PyCArrayB* self)
+{
+ // return viewing (!) numpy array
+ if(not self->ptrObj->range()){
+ PyErr_SetString(PyExc_RuntimeError, "array not initialized");
+ return NULL;
+ }
+ const SizeT d = self->ptrObj->range()->dim();
+ std::vector<npy_intp> dims(d);
+ /*
+ Py_INCREF(self); // keep data alive
+ PyObject* o = PyArray_SimpleNewFromData
+ ( static_cast<int>( d ) , dims.data(), self->ptrObj->typenum(), self->ptrObj->data() );
+ PyArray_BASE(o) = (PyObject*) self;
+ */
+ PyObject* o = PyArray_SimpleNew
+ ( static_cast<int>( d ) , dims.data(), self->ptrObj->typenum() );
+ void* data = PyArray_DATA(o);
+ const npy_intp s = PyArray_NBYTES(o);
+ if(s != self->ptrObj->datasize()) {
+ PyErr_SetString(PyExc_RuntimeError, "lib error");
+ }
+ memcpy( data, self->ptrObj->data(), self->ptrObj->datasize() );
+ return o;
}
PyMethodDef PyCArrayB_methods[] = {
- { "size", (PyCFunction) PyCArrayB_size, METH_VARARGS, "return size of the array" },
- { NULL }
+ { "size", (PyCFunction) PyCArrayB_size, METH_VARARGS| METH_KEYWORDS, "return size of the array" },
+ { "range", (PyCFunction) PyCArrayB_range, METH_VARARGS| METH_KEYWORDS, "return array range" },
+ { "writeFile", (PyCFunction) PyCArrayB_writeFile, METH_VARARGS| METH_KEYWORDS, "write array to file" },
+ { "readFile", (PyCFunction) PyCArrayB_readFile, METH_VARARGS| METH_KEYWORDS, "read array from file" },
+ { "npa", (PyCFunction) PyCArrayB_npa, METH_VARARGS| METH_KEYWORDS, "return numpy array (view)" },
+ { NULL, NULL, 0, NULL }
};
PyTypeObject PyCArrayBType = { PyVarObject_HEAD_INIT(NULL,0) "cnorxz.CArray" };
diff --git a/cnorxz/core/lib/range_wrapper.cpp b/cnorxz/core/lib/range_wrapper.cpp
index 184a886..38626a0 100644
--- a/cnorxz/core/lib/range_wrapper.cpp
+++ b/cnorxz/core/lib/range_wrapper.cpp
@@ -59,6 +59,8 @@ PyTypeObject* PyCRangeType_init()
PyCRangeType.tp_methods = PyCRange_methods;
PyCRangeType.tp_init = (initproc) PyCRange_init;
+ import_array();
+
if(PyType_Ready(&PyCRangeType) < 0){
return NULL;
}
diff --git a/setup.py b/setup.py
index 726b3ab..48b3b9f 100644
--- a/setup.py
+++ b/setup.py
@@ -1,7 +1,7 @@
#!/usr/bin/env python
-import Cython.Build
-#import setuptools
+#import numpy
+import setuptools
from distutils.core import setup, Extension
import sysconfig
import subprocess
@@ -27,6 +27,8 @@ inc_dirs = list()
if path_to_cnorxz != "":
inc_dirs.append( path_to_cnorxz + "/include/cnorxz" )
inc_dirs.append( "cnorxz/core/include" )
+#inc_dirs.append( numpy.get_include() )
+inc_dirs.append( "/home/chizeta/my_env/lib/python3.11/site-packages/numpy/core/include" )
lib_dirs = list()
lib_dirs.append( "/usr/lib" )
@@ -37,6 +39,7 @@ lib_dirs.append( "/home/chizeta/repos/cnorxz/install/lib" )
extra_compile_args = sysconfig.get_config_var('CFLAGS').split()
cnorxz_flags = subprocess.run([path_to_cnorxz+"/bin/cnorxz-config",'--flags'],stdout=subprocess.PIPE).stdout.decode('ascii').split()
+cnorxz_flags.remove("-Werror")
extra_compile_args += cnorxz_flags
default_extension_args = dict(