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switch to numpy 1.7 or later
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this requires some api changes in the typemap
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@vigsterkr
vigsterkr committed Feb 12, 2018
1 parent 1a314a6 commit 72455e8
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Showing 6 changed files with 55 additions and 55 deletions.
2 changes: 1 addition & 1 deletion src/interfaces/python/CMakeLists.txt
View file
@@ -1,7 +1,7 @@
# find python library for the found python interpreter
# i.e. versions should match!
FIND_PACKAGE(PythonLibs ${PYTHON_VERSION_STRING} EXACT REQUIRED)
FIND_PACKAGE(NumPy REQUIRED)
FIND_PACKAGE(NumPy 1.7 REQUIRED)

SET(HAVE_PYTHON 1)

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6 changes: 3 additions & 3 deletions src/interfaces/python/CustomKernel_protocols.i
View file
Expand Up @@ -209,7 +209,7 @@ static PyObject* class_name ## _getitem(PyObject *self, Py_ssize_t idx)
ret=(PyArrayObject *) PyArray_NewFromDescr(&PyArray_Type, descr,
1, shape+1,
strides+1, data,
NPY_FARRAY | NPY_WRITEABLE,
NPY_ARRAY_FARRAY | NPY_ARRAY_WRITEABLE,
(PyObject *) self);
if (ret==NULL)
goto fail;
Expand Down Expand Up @@ -297,7 +297,7 @@ static PyObject* class_name ## _getslice(PyObject *self, Py_ssize_t ilow, Py_ssi
ret=(PyArrayObject *) PyArray_NewFromDescr(&PyArray_Type, descr,
2, shape,
strides, data,
NPY_FARRAY | NPY_WRITEABLE,
NPY_ARRAY_FARRAY | NPY_ARRAY_WRITEABLE,
(PyObject *) self);
if (ret==NULL)
goto fail;
Expand Down Expand Up @@ -454,7 +454,7 @@ static PyObject* class_name ## _getsubscript(PyObject *self, PyObject *key, bool
ret=(PyObject *) PyArray_NewFromDescr(&PyArray_Type, descr,
ndims, shape,
strides, data,
NPY_FARRAY | NPY_WRITEABLE,
NPY_ARRAY_FARRAY | NPY_ARRAY_WRITEABLE,
(PyObject *) self);
}

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6 changes: 3 additions & 3 deletions src/interfaces/python/DenseFeatures_protocols.i
View file
Expand Up @@ -203,7 +203,7 @@ static PyObject* class_name ## _getitem(PyObject *self, Py_ssize_t idx)
ret=(PyArrayObject *) PyArray_NewFromDescr(&PyArray_Type, descr,
1, shape+1,
strides+1, data,
NPY_FARRAY | NPY_WRITEABLE,
NPY_ARRAY_FARRAY | NPY_ARRAY_WRITEABLE,
(PyObject *) self);
if (ret==NULL)
goto fail;
Expand Down Expand Up @@ -291,7 +291,7 @@ static PyObject* class_name ## _getslice(PyObject *self, Py_ssize_t ilow, Py_ssi
ret=(PyArrayObject *) PyArray_NewFromDescr(&PyArray_Type, descr,
2, shape,
strides, data,
NPY_FARRAY | NPY_WRITEABLE,
NPY_ARRAY_FARRAY | NPY_ARRAY_WRITEABLE,
(PyObject *) self);
if (ret==NULL)
goto fail;
Expand Down Expand Up @@ -448,7 +448,7 @@ static PyObject* class_name ## _getsubscript(PyObject *self, PyObject *key, bool
ret=(PyObject *) PyArray_NewFromDescr(&PyArray_Type, descr,
ndims, shape,
strides, data,
NPY_FARRAY | NPY_WRITEABLE,
NPY_ARRAY_FARRAY | NPY_ARRAY_WRITEABLE,
(PyObject *) self);
}

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4 changes: 2 additions & 2 deletions src/interfaces/python/DenseLabels_protocols.i
View file
Expand Up @@ -202,7 +202,7 @@ static PyObject* class_name ## _getitem(PyObject *self, Py_ssize_t idx, bool get
ret=(PyObject *) PyArray_NewFromDescr(&PyArray_Type, descr,
0, shape,
strides, data,
NPY_FARRAY | NPY_WRITEABLE,
NPY_ARRAY_FARRAY | NPY_ARRAY_WRITEABLE,
(PyObject *) self);
}

Expand Down Expand Up @@ -289,7 +289,7 @@ static PyObject* class_name ## _getslice(PyObject *self, Py_ssize_t ilow, Py_ssi
ret=(PyArrayObject *) PyArray_NewFromDescr(&PyArray_Type, descr,
1, shape,
strides, data,
NPY_FARRAY | NPY_WRITEABLE,
NPY_ARRAY_FARRAY | NPY_ARRAY_WRITEABLE,
(PyObject *) self);
if (ret==NULL)
goto fail;
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4 changes: 2 additions & 2 deletions src/interfaces/python/SGVector_protocols.i
View file
Expand Up @@ -201,7 +201,7 @@ static PyObject* class_name ## _getitem(PyObject *self, Py_ssize_t idx, bool get
ret=(PyObject *) PyArray_NewFromDescr(&PyArray_Type, descr,
0, shape,
strides, data,
NPY_FARRAY | NPY_WRITEABLE,
NPY_ARRAY_FARRAY | NPY_ARRAY_WRITEABLE,
(PyObject *) self);
}

Expand Down Expand Up @@ -288,7 +288,7 @@ static PyObject* class_name ## _getslice(PyObject *self, Py_ssize_t ilow, Py_ssi
ret=(PyArrayObject *) PyArray_NewFromDescr(&PyArray_Type, descr,
1, shape,
strides, data,
NPY_FARRAY | NPY_WRITEABLE,
NPY_ARRAY_FARRAY | NPY_ARRAY_WRITEABLE,
(PyObject *) self);
if (ret==NULL)
goto fail;
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88 changes: 44 additions & 44 deletions src/interfaces/python/swig_typemaps.i
View file
Expand Up @@ -29,6 +29,7 @@
#include <shogun/lib/memory.h>

#undef _POSIX_C_SOURCE
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
extern "C" {
#include <Python.h>
#include <numpy/arrayobject.h>
Expand All @@ -37,10 +38,8 @@ extern "C" {
/* Functions to extract array attributes.
*/
static bool is_array(PyObject* a) { return (a) && PyArray_Check(a); }
static int array_type(PyObject* a) { return (int) PyArray_TYPE(a); }
static int array_dimensions(PyObject* a) { return ((PyArrayObject *)a)->nd; }
static int array_size(PyObject* a, int i) { return ((PyArrayObject *)a)->dimensions[i]; }
static bool array_is_contiguous(PyObject* a) { return PyArray_ISCONTIGUOUS(a); }
static int array_type(const PyObject* a) { return (int) PyArray_TYPE((const PyArrayObject*)a); }
static int array_dimensions(const PyObject* a) { return PyArray_NDIM((const PyArrayObject *)a); }

/* Given a PyObject, return a string describing its type.
*/
Expand Down Expand Up @@ -96,18 +95,18 @@ static const char* typecode_string(int typecode) {
* If array is NULL or dimensionality or typecode does not match
* return NULL
*/
static PyObject* make_contiguous(PyObject* ary, int* is_new_object,
int dims, int typecode, bool force_copy=false)
static PyArrayObject* make_contiguous(
PyObject* ary, int* is_new_object, int dims, int typecode, bool force_copy=false)
{
PyObject* array;
if (PyArray_ISFARRAY(ary) && !force_copy)
if (PyArray_ISFARRAY((PyArrayObject*)ary) && !force_copy)
{
array = ary;
*is_new_object = 0;
}
else
{
array=PyArray_FromAny((PyObject*)ary, NULL,0,0, NPY_FARRAY|NPY_ENSURECOPY, NULL);
array=PyArray_FromAny((PyObject*)ary, NULL,0,0, NPY_ARRAY_FARRAY|NPY_ARRAY_ENSURECOPY, NULL);
*is_new_object = 1;
}

Expand Down Expand Up @@ -151,7 +150,7 @@ static PyObject* make_contiguous(PyObject* ary, int* is_new_object,
return NULL;
}

return array;
return (PyArrayObject*)array;
}

/* End John Hunter translation (with modifications by Bill Spotz) */
Expand Down Expand Up @@ -244,12 +243,12 @@ static bool vector_from_numpy(SGVector<type>& sg_vec, PyObject* obj, int typecod
}

int is_new_object;
PyObject* array = make_contiguous(obj, &is_new_object, 1,typecode, true);
PyArrayObject* array = make_contiguous(obj, &is_new_object, 1,typecode, true);
if (!array)
return false;

((PyArrayObject*) array)->flags &= (-1 ^ NPY_OWNDATA);
type* vec = (type*) PyArray_BYTES(array);
PyArray_CLEARFLAGS(array, NPY_ARRAY_OWNDATA);
type* vec = (type*) PyArray_DATA(array);
int32_t vlen = PyArray_DIM(array,0);
Py_DECREF(array);

Expand All @@ -268,8 +267,8 @@ static bool vector_to_numpy(PyObject* &obj, SGVector<type> sg_vec, int typecode)
{
void* copy=get_copy(sg_vec.vector, sizeof(type)*size_t(sg_vec.vlen));
obj = PyArray_NewFromDescr(&PyArray_Type,
descr, 1, &dims, NULL, copy, NPY_FARRAY | NPY_WRITEABLE, NULL);
((PyArrayObject*) obj)->flags |= NPY_OWNDATA;
descr, 1, &dims, NULL, copy, NPY_ARRAY_FARRAY | NPY_ARRAY_WRITEABLE, NULL);
PyArray_ENABLEFLAGS((PyArrayObject*) obj, NPY_ARRAY_OWNDATA);
}

return descr!=NULL;
Expand All @@ -285,14 +284,14 @@ static bool matrix_from_numpy(SGMatrix<type>& sg_matrix, PyObject* obj, int type
}

int is_new_object;
PyObject* array = make_contiguous(obj, &is_new_object, 2,typecode, true);
PyArrayObject* array = make_contiguous(obj, &is_new_object, 2,typecode, true);
if (!array)
return false;

sg_matrix = shogun::SGMatrix<type>((type*) PyArray_BYTES(array),
sg_matrix = shogun::SGMatrix<type>((type*) PyArray_DATA(array),
PyArray_DIM(array,0), PyArray_DIM(array,1), true);

((PyArrayObject*) array)->flags &= (-1 ^ NPY_OWNDATA);
PyArray_CLEARFLAGS(array, NPY_ARRAY_OWNDATA);
Py_DECREF(array);

return true;
Expand All @@ -308,8 +307,8 @@ static bool matrix_to_numpy(PyObject* &obj, SGMatrix<type> sg_matrix, int typeco
{
void* copy=get_copy(sg_matrix.matrix, sizeof(type)*size_t(sg_matrix.num_rows)*size_t(sg_matrix.num_cols));
obj = PyArray_NewFromDescr(&PyArray_Type,
descr, 2, dims, NULL, (void*) copy, NPY_FARRAY | NPY_WRITEABLE, NULL);
((PyArrayObject*) obj)->flags |= NPY_OWNDATA;
descr, 2, dims, NULL, (void*) copy, NPY_ARRAY_FARRAY | NPY_ARRAY_WRITEABLE, NULL);
PyArray_ENABLEFLAGS((PyArrayObject*) obj, NPY_ARRAY_OWNDATA);
}

return descr!=NULL;
Expand All @@ -325,7 +324,7 @@ static bool array_from_numpy(SGNDArray<type>& sg_array, PyObject* obj, int typec
}

int is_new_object;
PyObject* array = make_contiguous(obj, &is_new_object, -1,typecode, true);
PyArrayObject* array = make_contiguous(obj, &is_new_object, -1,typecode, true);
if (!array)
return false;

Expand All @@ -340,9 +339,9 @@ static bool array_from_numpy(SGNDArray<type>& sg_array, PyObject* obj, int typec
for (int32_t i=0; i<ndim; i++)
temp_dims[i] = py_dims[i];

sg_array = SGNDArray<type>((type*) PyArray_BYTES(array), temp_dims, ndim);
sg_array = SGNDArray<type>((type*) PyArray_DATA(array), temp_dims, ndim);

((PyArrayObject*) array)->flags &= (-1 ^ NPY_OWNDATA);
PyArray_ENABLEFLAGS(array, NPY_ARRAY_OWNDATA);
Py_DECREF(array);

return true;
Expand All @@ -369,8 +368,8 @@ static bool array_to_numpy(PyObject* &obj, SGNDArray<type> sg_array, int typecod
{
void* copy=get_copy(sg_array.array, sizeof(type)*size_t(n));
obj = PyArray_NewFromDescr(&PyArray_Type,
descr, sg_array.num_dims, dims, NULL, (void*) copy, NPY_FARRAY | NPY_WRITEABLE, NULL);
((PyArrayObject*) obj)->flags |= NPY_OWNDATA;
descr, sg_array.num_dims, dims, NULL, (void*) copy, NPY_ARRAY_FARRAY | NPY_ARRAY_WRITEABLE, NULL);
PyArray_ENABLEFLAGS((PyArrayObject*) obj, NPY_ARRAY_OWNDATA);
}
#ifdef _MSC_VER
delete[] dims;
Expand Down Expand Up @@ -436,11 +435,11 @@ static bool string_from_strpy(SGStringList<type>& sg_strings, PyObject* obj, int
if (::is_array(o) && array_dimensions(o)==1 && array_type(o) == typecode)
{
int is_new_object=0;
PyObject* array = make_contiguous(o, &is_new_object, 1, typecode);
PyArrayObject* array = make_contiguous(o, &is_new_object, 1, typecode);
if (!array)
return false;

type* str=(type*) PyArray_BYTES(array);
type* str=(type*) PyArray_DATA(array);
int32_t len = PyArray_DIM(array,0);
max_len=shogun::CMath::max(len,max_len);

Expand Down Expand Up @@ -516,8 +515,8 @@ static bool string_to_strpy(PyObject* &obj, SGStringList<type> sg_strings, int t
npy_intp dims = str[i].slen;

s = PyArray_NewFromDescr(&PyArray_Type,
descr, 1, &dims, NULL, (void*) data, NPY_FARRAY | NPY_WRITEABLE, NULL);
((PyArrayObject*) s)->flags |= NPY_OWNDATA;
descr, 1, &dims, NULL, (void*) data, NPY_ARRAY_FARRAY | NPY_ARRAY_WRITEABLE, NULL);
PyArray_ENABLEFLAGS((PyArrayObject*) s, NPY_ARRAY_OWNDATA);
}
else
return false;
Expand Down Expand Up @@ -605,23 +604,23 @@ static bool spmatrix_from_numpy(SGSparseMatrix<type>& sg_matrix, PyObject* obj,

/* get indptr array */
int is_new_object_indptr=0;
PyObject* array_indptr = make_contiguous(indptr, &is_new_object_indptr, 1, NPY_INT32);
PyArrayObject* array_indptr = make_contiguous(indptr, &is_new_object_indptr, 1, NPY_INT32);
if (!array_indptr) return false;
int32_t* bytes_indptr=(int32_t*) PyArray_BYTES(array_indptr);
int32_t* bytes_indptr=(int32_t*) PyArray_DATA(array_indptr);
int32_t len_indptr = PyArray_DIM(array_indptr,0);

/* get indices array */
int is_new_object_indices=0;
PyObject* array_indices = make_contiguous(indices, &is_new_object_indices, 1, NPY_INT32);
PyArrayObject* array_indices = make_contiguous(indices, &is_new_object_indices, 1, NPY_INT32);
if (!array_indices) return false;
int32_t* bytes_indices=(int32_t*) PyArray_BYTES(array_indices);
int32_t* bytes_indices=(int32_t*) PyArray_DATA(array_indices);
int32_t len_indices = PyArray_DIM(array_indices,0);

/* get data array */
int is_new_object_data=0;
PyObject* array_data = make_contiguous(data, &is_new_object_data, 1, typecode);
PyArrayObject* array_data = make_contiguous(data, &is_new_object_data, 1, typecode);
if (!array_data) return false;
type* bytes_data=(type*) PyArray_BYTES(array_data);
type* bytes_data=(type*) PyArray_DATA(array_data);
int32_t len_data = PyArray_DIM(array_data,0);

if (len_indices!=len_data)
Expand Down Expand Up @@ -719,17 +718,17 @@ static bool spmatrix_to_numpy(PyObject* &obj, SGSparseMatrix<type> sg_matrix, in

npy_intp indptr_dims = num_vec+1;
indptr_py = PyArray_NewFromDescr(&PyArray_Type,
descr, 1, &indptr_dims, NULL, (void*) indptr, NPY_FARRAY | NPY_WRITEABLE, NULL);
((PyArrayObject*) indptr_py)->flags |= NPY_OWNDATA;
descr, 1, &indptr_dims, NULL, (void*) indptr, NPY_ARRAY_FARRAY | NPY_ARRAY_WRITEABLE, NULL);
PyArray_ENABLEFLAGS((PyArrayObject*) indptr_py, NPY_ARRAY_OWNDATA);

npy_intp dims = nnz;
indices_py = PyArray_NewFromDescr(&PyArray_Type,
descr, 1, &dims, NULL, (void*) indices, NPY_FARRAY | NPY_WRITEABLE, NULL);
((PyArrayObject*) indices_py)->flags |= NPY_OWNDATA;
descr, 1, &dims, NULL, (void*) indices, NPY_ARRAY_FARRAY | NPY_ARRAY_WRITEABLE, NULL);
PyArray_ENABLEFLAGS((PyArrayObject*) indices_py, NPY_ARRAY_OWNDATA);

data_py = PyArray_NewFromDescr(&PyArray_Type,
descr_data, 1, &dims, NULL, (void*) data, NPY_FARRAY | NPY_WRITEABLE, NULL);
((PyArrayObject*) data_py)->flags |= NPY_OWNDATA;
descr_data, 1, &dims, NULL, (void*) data, NPY_ARRAY_FARRAY | NPY_ARRAY_WRITEABLE, NULL);
PyArray_ENABLEFLAGS((PyArrayObject*) data_py, NPY_ARRAY_OWNDATA);

PyTuple_SetItem(tuple, 0, data_py);
PyTuple_SetItem(tuple, 1, indices_py);
Expand Down Expand Up @@ -778,12 +777,13 @@ static bool spvector_to_numpy(PyObject* &obj, SGSparseVector<type> sg_vector, in
}

indices_py = PyArray_NewFromDescr(&PyArray_Type,
descr, 1, &dims, NULL, (void*) indices, NPY_FARRAY | NPY_WRITEABLE, NULL);
((PyArrayObject*) indices_py)->flags |= NPY_OWNDATA;
descr, 1, &dims, NULL, (void*) indices, NPY_ARRAY_FARRAY | NPY_ARRAY_WRITEABLE, NULL);

PyArray_ENABLEFLAGS((PyArrayObject*) indices_py, NPY_ARRAY_OWNDATA);

data_py = PyArray_NewFromDescr(&PyArray_Type,
descr_data, 1, &dims, NULL, (void*) data, NPY_FARRAY | NPY_WRITEABLE, NULL);
((PyArrayObject*) data_py)->flags |= NPY_OWNDATA;
descr_data, 1, &dims, NULL, (void*) data, NPY_ARRAY_FARRAY | NPY_ARRAY_WRITEABLE, NULL);
PyArray_ENABLEFLAGS((PyArrayObject*) data_py, NPY_ARRAY_OWNDATA);

PyTuple_SetItem(tuple, 0, data_py);
PyTuple_SetItem(tuple, 1, indices_py);
Expand Down

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