diff --git a/setup.py b/setup.py
index cd50adb580831137db05566c781ce92f6f588229..1e4fe3a4765e3a7de578c3522cdc30a5841d6b71 100755
--- a/setup.py
+++ b/setup.py
@@ -23,9 +23,8 @@ setup(
packages=find_packages(exclude=('tests', 'docs')),
ext_modules=cythonize([
"src/screening/utils.pyx",
- "src/screening/gap_ptest.pyx",
- "src/screening/gap_rqtest.pyx",
- "src/screening/kappa_test.pyx",
+ "src/screening/gap_test_all.pyx",
+ "src/screening/gap_test_p_1.pyx",
]),
)
diff --git a/src/__version.py b/src/__version.py
index 89d2d61ac5f9d313dcd5a3f669a61eafd7775ba1..47c8f9dd2d2d6e5a2a5203e2c37979e3049b5f24 100755
--- a/src/__version.py
+++ b/src/__version.py
@@ -1,3 +1,3 @@
# -*- coding: utf-8 -*-
-__version__ = "0.9.0"
\ No newline at end of file
+__version__ = "2.0.0"
\ No newline at end of file
diff --git a/src/screening/ascreening.py b/src/screening/ascreening.py
index c1d8c82264f59b583101f3d5498e5c01dcabc887..b20a23a02ecbaf7f7917d6d19b55f220aa597329 100644
--- a/src/screening/ascreening.py
+++ b/src/screening/ascreening.py
@@ -12,18 +12,16 @@ class AbstractGapScreening(ABC):
self.name = "NONAME"
- def get_name(self):
- return self.name
-
-
@abstractmethod
- def apply_test(self, Atu_abs, gap, lbd, vec_gammas, offset_radius=0, index=None) -> np.ndarray:
+ def apply_test(self, Atu_abs, gap, lbd, vec_gammas, coeff_dual_scaling=1., offset_radius=0, index=None) -> np.ndarray:
""" GAP Sphere screening test detailed in Cédric's node
Parameters
----------
Atu_abs : np.ndarray
- vector |matA.T @ vecu| where vecu is dual admissible
+ vector |matA.T @ vecu|
+ vecu is not necessarily dual admissible
+ In that case, the dual scaling factor must be provided
size [n]
gap : positive float
duality gap
@@ -32,6 +30,11 @@ class AbstractGapScreening(ABC):
vec_gammas : np.ndarray
slope parameters
size [n,]
+ coeff_dual_scaling : positif float
+ If coeff_dual_scaling is not feasible, dual scaling factor
+ such taht vecu / coeff_dual_scaling os dual feasible
+ Here for code optimization purposes
+ Default value is 1. (vecu is feasible)
offset_radius : float
additive term added to the redius
index : np.ndarray
diff --git a/src/screening/gap_rqtest.c b/src/screening/gap_rqtest.c
deleted file mode 100644
index 55d93670a7bd5fa4656c61472d5b2e317a481a32..0000000000000000000000000000000000000000
--- a/src/screening/gap_rqtest.c
+++ /dev/null
@@ -1,8083 +0,0 @@
-/* Generated by Cython 0.29.24 */
-
-/* BEGIN: Cython Metadata
-{
- "distutils": {
- "depends": [],
- "name": "src.screening.gap_rqtest",
- "sources": [
- "src/screening/gap_rqtest.pyx"
- ]
- },
- "module_name": "src.screening.gap_rqtest"
-}
-END: Cython Metadata */
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- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
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-#endif
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- #define PyInt_CheckExact(op) PyLong_CheckExact(op)
- #define PyInt_FromString PyLong_FromString
- #define PyInt_FromUnicode PyLong_FromUnicode
- #define PyInt_FromLong PyLong_FromLong
- #define PyInt_FromSize_t PyLong_FromSize_t
- #define PyInt_FromSsize_t PyLong_FromSsize_t
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-#if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY
- #ifndef PyUnicode_InternFromString
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- typedef long Py_hash_t;
- #define __Pyx_PyInt_FromHash_t PyInt_FromLong
- #define __Pyx_PyInt_AsHash_t PyInt_AsLong
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- #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
- #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
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- #define __Pyx_PyMethod_New(func, self, klass) ((self) ? ((void)(klass), PyMethod_New(func, self)) : __Pyx_NewRef(func))
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- #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass)
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- #define __Pyx_PyType_AsAsync(obj) NULL
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-#ifndef __Pyx_PyAsyncMethodsStruct
- typedef struct {
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- unaryfunc am_anext;
- } __Pyx_PyAsyncMethodsStruct;
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-
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- #define _USE_MATH_DEFINES
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-#include <math.h>
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-#define __PYX_NAN() ((float) NAN)
-#else
-static CYTHON_INLINE float __PYX_NAN() {
- float value;
- memset(&value, 0xFF, sizeof(value));
- return value;
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-#if defined(__CYGWIN__) && defined(_LDBL_EQ_DBL)
-#define __Pyx_truncl trunc
-#else
-#define __Pyx_truncl truncl
-#endif
-
-#define __PYX_MARK_ERR_POS(f_index, lineno) \
- { __pyx_filename = __pyx_f[f_index]; (void)__pyx_filename; __pyx_lineno = lineno; (void)__pyx_lineno; __pyx_clineno = __LINE__; (void)__pyx_clineno; }
-#define __PYX_ERR(f_index, lineno, Ln_error) \
- { __PYX_MARK_ERR_POS(f_index, lineno) goto Ln_error; }
-
-#ifndef __PYX_EXTERN_C
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- #define __PYX_EXTERN_C extern "C"
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- #define __PYX_EXTERN_C extern
- #endif
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-
-#define __PYX_HAVE__src__screening__gap_rqtest
-#define __PYX_HAVE_API__src__screening__gap_rqtest
-/* Early includes */
-#include <string.h>
-#include <stdio.h>
-#include "numpy/arrayobject.h"
-#include "numpy/ndarrayobject.h"
-#include "numpy/ndarraytypes.h"
-#include "numpy/arrayscalars.h"
-#include "numpy/ufuncobject.h"
-
- /* NumPy API declarations from "numpy/__init__.pxd" */
-
-#ifdef _OPENMP
-#include <omp.h>
-#endif /* _OPENMP */
-
-#if defined(PYREX_WITHOUT_ASSERTIONS) && !defined(CYTHON_WITHOUT_ASSERTIONS)
-#define CYTHON_WITHOUT_ASSERTIONS
-#endif
-
-typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding;
- const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry;
-
-#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
-#define __PYX_DEFAULT_STRING_ENCODING_IS_UTF8 0
-#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT (PY_MAJOR_VERSION >= 3 && __PYX_DEFAULT_STRING_ENCODING_IS_UTF8)
-#define __PYX_DEFAULT_STRING_ENCODING ""
-#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
-#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#define __Pyx_uchar_cast(c) ((unsigned char)c)
-#define __Pyx_long_cast(x) ((long)x)
-#define __Pyx_fits_Py_ssize_t(v, type, is_signed) (\
- (sizeof(type) < sizeof(Py_ssize_t)) ||\
- (sizeof(type) > sizeof(Py_ssize_t) &&\
- likely(v < (type)PY_SSIZE_T_MAX ||\
- v == (type)PY_SSIZE_T_MAX) &&\
- (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\
- v == (type)PY_SSIZE_T_MIN))) ||\
- (sizeof(type) == sizeof(Py_ssize_t) &&\
- (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\
- v == (type)PY_SSIZE_T_MAX))) )
-static CYTHON_INLINE int __Pyx_is_valid_index(Py_ssize_t i, Py_ssize_t limit) {
- return (size_t) i < (size_t) limit;
-}
-#if defined (__cplusplus) && __cplusplus >= 201103L
- #include <cstdlib>
- #define __Pyx_sst_abs(value) std::abs(value)
-#elif SIZEOF_INT >= SIZEOF_SIZE_T
- #define __Pyx_sst_abs(value) abs(value)
-#elif SIZEOF_LONG >= SIZEOF_SIZE_T
- #define __Pyx_sst_abs(value) labs(value)
-#elif defined (_MSC_VER)
- #define __Pyx_sst_abs(value) ((Py_ssize_t)_abs64(value))
-#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
- #define __Pyx_sst_abs(value) llabs(value)
-#elif defined (__GNUC__)
- #define __Pyx_sst_abs(value) __builtin_llabs(value)
-#else
- #define __Pyx_sst_abs(value) ((value<0) ? -value : value)
-#endif
-static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject*);
-static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
-#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
-#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l)
-#define __Pyx_PyBytes_FromString PyBytes_FromString
-#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*);
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString
- #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#else
- #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString
- #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize
-#endif
-#define __Pyx_PyBytes_AsWritableString(s) ((char*) PyBytes_AS_STRING(s))
-#define __Pyx_PyBytes_AsWritableSString(s) ((signed char*) PyBytes_AS_STRING(s))
-#define __Pyx_PyBytes_AsWritableUString(s) ((unsigned char*) PyBytes_AS_STRING(s))
-#define __Pyx_PyBytes_AsString(s) ((const char*) PyBytes_AS_STRING(s))
-#define __Pyx_PyBytes_AsSString(s) ((const signed char*) PyBytes_AS_STRING(s))
-#define __Pyx_PyBytes_AsUString(s) ((const unsigned char*) PyBytes_AS_STRING(s))
-#define __Pyx_PyObject_AsWritableString(s) ((char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_AsWritableSString(s) ((signed char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_AsWritableUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_AsSString(s) ((const signed char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_AsUString(s) ((const unsigned char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s)
-#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s)
-#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s)
-#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s)
-#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s)
-static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) {
- const Py_UNICODE *u_end = u;
- while (*u_end++) ;
- return (size_t)(u_end - u - 1);
-}
-#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
-#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
-#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode
-#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj)
-#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None)
-static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b);
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
-static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject*);
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x);
-#define __Pyx_PySequence_Tuple(obj)\
- (likely(PyTuple_CheckExact(obj)) ? __Pyx_NewRef(obj) : PySequence_Tuple(obj))
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
-#if CYTHON_ASSUME_SAFE_MACROS
-#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
-#else
-#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
-#endif
-#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
-#if PY_MAJOR_VERSION >= 3
-#define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x))
-#else
-#define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x))
-#endif
-#define __Pyx_PyNumber_Float(x) (PyFloat_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Float(x))
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
-static int __Pyx_sys_getdefaultencoding_not_ascii;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys;
- PyObject* default_encoding = NULL;
- PyObject* ascii_chars_u = NULL;
- PyObject* ascii_chars_b = NULL;
- const char* default_encoding_c;
- sys = PyImport_ImportModule("sys");
- if (!sys) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL);
- Py_DECREF(sys);
- if (!default_encoding) goto bad;
- default_encoding_c = PyBytes_AsString(default_encoding);
- if (!default_encoding_c) goto bad;
- if (strcmp(default_encoding_c, "ascii") == 0) {
- __Pyx_sys_getdefaultencoding_not_ascii = 0;
- } else {
- char ascii_chars[128];
- int c;
- for (c = 0; c < 128; c++) {
- ascii_chars[c] = c;
- }
- __Pyx_sys_getdefaultencoding_not_ascii = 1;
- ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
- if (!ascii_chars_u) goto bad;
- ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
- if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
- PyErr_Format(
- PyExc_ValueError,
- "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.",
- default_encoding_c);
- goto bad;
- }
- Py_DECREF(ascii_chars_u);
- Py_DECREF(ascii_chars_b);
- }
- Py_DECREF(default_encoding);
- return 0;
-bad:
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- Py_XDECREF(ascii_chars_u);
- Py_XDECREF(ascii_chars_b);
- return -1;
-}
-#endif
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
-#else
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
-static char* __PYX_DEFAULT_STRING_ENCODING;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys;
- PyObject* default_encoding = NULL;
- char* default_encoding_c;
- sys = PyImport_ImportModule("sys");
- if (!sys) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
- Py_DECREF(sys);
- if (!default_encoding) goto bad;
- default_encoding_c = PyBytes_AsString(default_encoding);
- if (!default_encoding_c) goto bad;
- __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c) + 1);
- if (!__PYX_DEFAULT_STRING_ENCODING) goto bad;
- strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
- Py_DECREF(default_encoding);
- return 0;
-bad:
- Py_XDECREF(default_encoding);
- return -1;
-}
-#endif
-#endif
-
-
-/* Test for GCC > 2.95 */
-#if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)))
- #define likely(x) __builtin_expect(!!(x), 1)
- #define unlikely(x) __builtin_expect(!!(x), 0)
-#else /* !__GNUC__ or GCC < 2.95 */
- #define likely(x) (x)
- #define unlikely(x) (x)
-#endif /* __GNUC__ */
-static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; }
-
-static PyObject *__pyx_m = NULL;
-static PyObject *__pyx_d;
-static PyObject *__pyx_b;
-static PyObject *__pyx_cython_runtime = NULL;
-static PyObject *__pyx_empty_tuple;
-static PyObject *__pyx_empty_bytes;
-static PyObject *__pyx_empty_unicode;
-static int __pyx_lineno;
-static int __pyx_clineno = 0;
-static const char * __pyx_cfilenm= __FILE__;
-static const char *__pyx_filename;
-
-/* Header.proto */
-#if !defined(CYTHON_CCOMPLEX)
- #if defined(__cplusplus)
- #define CYTHON_CCOMPLEX 1
- #elif defined(_Complex_I)
- #define CYTHON_CCOMPLEX 1
- #else
- #define CYTHON_CCOMPLEX 0
- #endif
-#endif
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- #include <complex>
- #else
- #include <complex.h>
- #endif
-#endif
-#if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__)
- #undef _Complex_I
- #define _Complex_I 1.0fj
-#endif
-
-
-static const char *__pyx_f[] = {
- "src/screening/gap_rqtest.pyx",
- "stringsource",
- "venv/lib/python3.8/site-packages/numpy/__init__.pxd",
- "venv/lib/python3.8/site-packages/Cython/Includes/cpython/type.pxd",
-};
-/* BufferFormatStructs.proto */
-#define IS_UNSIGNED(type) (((type) -1) > 0)
-struct __Pyx_StructField_;
-#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0)
-typedef struct {
- const char* name;
- struct __Pyx_StructField_* fields;
- size_t size;
- size_t arraysize[8];
- int ndim;
- char typegroup;
- char is_unsigned;
- int flags;
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-typedef struct __Pyx_StructField_ {
- __Pyx_TypeInfo* type;
- const char* name;
- size_t offset;
-} __Pyx_StructField;
-typedef struct {
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-typedef struct {
- __Pyx_StructField root;
- __Pyx_BufFmt_StackElem* head;
- size_t fmt_offset;
- size_t new_count, enc_count;
- size_t struct_alignment;
- int is_complex;
- char enc_type;
- char new_packmode;
- char enc_packmode;
- char is_valid_array;
-} __Pyx_BufFmt_Context;
-
-
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":690
- * # in Cython to enable them only on the right systems.
- *
- * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<<
- * ctypedef npy_int16 int16_t
- * ctypedef npy_int32 int32_t
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-typedef npy_int8 __pyx_t_5numpy_int8_t;
-
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":691
- *
- * ctypedef npy_int8 int8_t
- * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<<
- * ctypedef npy_int32 int32_t
- * ctypedef npy_int64 int64_t
- */
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- ((void)__Pyx_BUILD_ASSERT_EXPR(sizeof(PyFrameObject) == offsetof(PyFrameObject, f_localsplus) + Py_MEMBER_SIZE(PyFrameObject, f_localsplus)),\
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- #define __Pyx_PyFrame_GetLocalsplus(frame)\
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-/* PyObjectCall.proto */
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-#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw)
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-
-/* PyObjectCall2Args.proto */
-static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2);
-
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-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg);
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-
-/* PyObjectCallOneArg.proto */
-static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg);
-
-/* ExtTypeTest.proto */
-static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type);
-
-/* BufferFallbackError.proto */
-static void __Pyx_RaiseBufferFallbackError(void);
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-/* GetItemInt.proto */
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- (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL))
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
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-#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
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-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
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-static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j);
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
- int is_list, int wraparound, int boundscheck);
-
-/* ObjectGetItem.proto */
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-static CYTHON_INLINE PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key);
-#else
-#define __Pyx_PyObject_GetItem(obj, key) PyObject_GetItem(obj, key)
-#endif
-
-/* RaiseException.proto */
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause);
-
-/* GetTopmostException.proto */
-#if CYTHON_USE_EXC_INFO_STACK
-static _PyErr_StackItem * __Pyx_PyErr_GetTopmostException(PyThreadState *tstate);
-#endif
-
-/* SaveResetException.proto */
-#if CYTHON_FAST_THREAD_STATE
-#define __Pyx_ExceptionSave(type, value, tb) __Pyx__ExceptionSave(__pyx_tstate, type, value, tb)
-static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
-#define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb)
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-#else
-#define __Pyx_ExceptionSave(type, value, tb) PyErr_GetExcInfo(type, value, tb)
-#define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb)
-#endif
-
-/* PyErrExceptionMatches.proto */
-#if CYTHON_FAST_THREAD_STATE
-#define __Pyx_PyErr_ExceptionMatches(err) __Pyx_PyErr_ExceptionMatchesInState(__pyx_tstate, err)
-static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err);
-#else
-#define __Pyx_PyErr_ExceptionMatches(err) PyErr_ExceptionMatches(err)
-#endif
-
-/* GetException.proto */
-#if CYTHON_FAST_THREAD_STATE
-#define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb)
-static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
-#else
-static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb);
-#endif
-
-/* PyObject_GenericGetAttrNoDict.proto */
-#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000
-static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name);
-#else
-#define __Pyx_PyObject_GenericGetAttrNoDict PyObject_GenericGetAttr
-#endif
-
-/* PyObject_GenericGetAttr.proto */
-#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000
-static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name);
-#else
-#define __Pyx_PyObject_GenericGetAttr PyObject_GenericGetAttr
-#endif
-
-/* PyObjectGetAttrStrNoError.proto */
-static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name);
-
-/* SetupReduce.proto */
-static int __Pyx_setup_reduce(PyObject* type_obj);
-
-/* TypeImport.proto */
-#ifndef __PYX_HAVE_RT_ImportType_proto
-#define __PYX_HAVE_RT_ImportType_proto
-enum __Pyx_ImportType_CheckSize {
- __Pyx_ImportType_CheckSize_Error = 0,
- __Pyx_ImportType_CheckSize_Warn = 1,
- __Pyx_ImportType_CheckSize_Ignore = 2
-};
-static PyTypeObject *__Pyx_ImportType(PyObject* module, const char *module_name, const char *class_name, size_t size, enum __Pyx_ImportType_CheckSize check_size);
-#endif
-
-/* Import.proto */
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level);
-
-/* ImportFrom.proto */
-static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name);
-
-/* CLineInTraceback.proto */
-#ifdef CYTHON_CLINE_IN_TRACEBACK
-#define __Pyx_CLineForTraceback(tstate, c_line) (((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0)
-#else
-static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line);
-#endif
-
-/* CodeObjectCache.proto */
-typedef struct {
- PyCodeObject* code_object;
- int code_line;
-} __Pyx_CodeObjectCacheEntry;
-struct __Pyx_CodeObjectCache {
- int count;
- int max_count;
- __Pyx_CodeObjectCacheEntry* entries;
-};
-static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
-static PyCodeObject *__pyx_find_code_object(int code_line);
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
-
-/* AddTraceback.proto */
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename);
-
-/* BufferStructDeclare.proto */
-typedef struct {
- Py_ssize_t shape, strides, suboffsets;
-} __Pyx_Buf_DimInfo;
-typedef struct {
- size_t refcount;
- Py_buffer pybuffer;
-} __Pyx_Buffer;
-typedef struct {
- __Pyx_Buffer *rcbuffer;
- char *data;
- __Pyx_Buf_DimInfo diminfo[8];
-} __Pyx_LocalBuf_ND;
-
-#if PY_MAJOR_VERSION < 3
- static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags);
- static void __Pyx_ReleaseBuffer(Py_buffer *view);
-#else
- #define __Pyx_GetBuffer PyObject_GetBuffer
- #define __Pyx_ReleaseBuffer PyBuffer_Release
-#endif
-
-
-/* GCCDiagnostics.proto */
-#if defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 6))
-#define __Pyx_HAS_GCC_DIAGNOSTIC
-#endif
-
-/* RealImag.proto */
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- #define __Pyx_CREAL(z) ((z).real())
- #define __Pyx_CIMAG(z) ((z).imag())
- #else
- #define __Pyx_CREAL(z) (__real__(z))
- #define __Pyx_CIMAG(z) (__imag__(z))
- #endif
-#else
- #define __Pyx_CREAL(z) ((z).real)
- #define __Pyx_CIMAG(z) ((z).imag)
-#endif
-#if defined(__cplusplus) && CYTHON_CCOMPLEX\
- && (defined(_WIN32) || defined(__clang__) || (defined(__GNUC__) && (__GNUC__ >= 5 || __GNUC__ == 4 && __GNUC_MINOR__ >= 4 )) || __cplusplus >= 201103)
- #define __Pyx_SET_CREAL(z,x) ((z).real(x))
- #define __Pyx_SET_CIMAG(z,y) ((z).imag(y))
-#else
- #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x)
- #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y)
-#endif
-
-/* Arithmetic.proto */
-#if CYTHON_CCOMPLEX
- #define __Pyx_c_eq_float(a, b) ((a)==(b))
- #define __Pyx_c_sum_float(a, b) ((a)+(b))
- #define __Pyx_c_diff_float(a, b) ((a)-(b))
- #define __Pyx_c_prod_float(a, b) ((a)*(b))
- #define __Pyx_c_quot_float(a, b) ((a)/(b))
- #define __Pyx_c_neg_float(a) (-(a))
- #ifdef __cplusplus
- #define __Pyx_c_is_zero_float(z) ((z)==(float)0)
- #define __Pyx_c_conj_float(z) (::std::conj(z))
- #if 1
- #define __Pyx_c_abs_float(z) (::std::abs(z))
- #define __Pyx_c_pow_float(a, b) (::std::pow(a, b))
- #endif
- #else
- #define __Pyx_c_is_zero_float(z) ((z)==0)
- #define __Pyx_c_conj_float(z) (conjf(z))
- #if 1
- #define __Pyx_c_abs_float(z) (cabsf(z))
- #define __Pyx_c_pow_float(a, b) (cpowf(a, b))
- #endif
- #endif
-#else
- static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex, __pyx_t_float_complex);
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex, __pyx_t_float_complex);
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex, __pyx_t_float_complex);
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex, __pyx_t_float_complex);
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex, __pyx_t_float_complex);
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex);
- static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex);
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex);
- #if 1
- static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex);
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex, __pyx_t_float_complex);
- #endif
-#endif
-
-/* Arithmetic.proto */
-#if CYTHON_CCOMPLEX
- #define __Pyx_c_eq_double(a, b) ((a)==(b))
- #define __Pyx_c_sum_double(a, b) ((a)+(b))
- #define __Pyx_c_diff_double(a, b) ((a)-(b))
- #define __Pyx_c_prod_double(a, b) ((a)*(b))
- #define __Pyx_c_quot_double(a, b) ((a)/(b))
- #define __Pyx_c_neg_double(a) (-(a))
- #ifdef __cplusplus
- #define __Pyx_c_is_zero_double(z) ((z)==(double)0)
- #define __Pyx_c_conj_double(z) (::std::conj(z))
- #if 1
- #define __Pyx_c_abs_double(z) (::std::abs(z))
- #define __Pyx_c_pow_double(a, b) (::std::pow(a, b))
- #endif
- #else
- #define __Pyx_c_is_zero_double(z) ((z)==0)
- #define __Pyx_c_conj_double(z) (conj(z))
- #if 1
- #define __Pyx_c_abs_double(z) (cabs(z))
- #define __Pyx_c_pow_double(a, b) (cpow(a, b))
- #endif
- #endif
-#else
- static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex, __pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex, __pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex, __pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex, __pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex, __pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex);
- static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex);
- #if 1
- static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex, __pyx_t_double_complex);
- #endif
-#endif
-
-/* CIntToPy.proto */
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value);
-
-/* CIntFromPy.proto */
-static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *);
-
-/* CIntToPy.proto */
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value);
-
-/* CIntFromPy.proto */
-static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *);
-
-/* FastTypeChecks.proto */
-#if CYTHON_COMPILING_IN_CPYTHON
-#define __Pyx_TypeCheck(obj, type) __Pyx_IsSubtype(Py_TYPE(obj), (PyTypeObject *)type)
-static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b);
-static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject *type);
-static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *type1, PyObject *type2);
-#else
-#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
-#define __Pyx_PyErr_GivenExceptionMatches(err, type) PyErr_GivenExceptionMatches(err, type)
-#define __Pyx_PyErr_GivenExceptionMatches2(err, type1, type2) (PyErr_GivenExceptionMatches(err, type1) || PyErr_GivenExceptionMatches(err, type2))
-#endif
-#define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception)
-
-/* CheckBinaryVersion.proto */
-static int __Pyx_check_binary_version(void);
-
-/* InitStrings.proto */
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t);
-
-
-/* Module declarations from 'cpython.buffer' */
-
-/* Module declarations from 'libc.string' */
-
-/* Module declarations from 'libc.stdio' */
-
-/* Module declarations from '__builtin__' */
-
-/* Module declarations from 'cpython.type' */
-static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0;
-
-/* Module declarations from 'cpython' */
-
-/* Module declarations from 'cpython.object' */
-
-/* Module declarations from 'cpython.ref' */
-
-/* Module declarations from 'cpython.mem' */
-
-/* Module declarations from 'numpy' */
-
-/* Module declarations from 'numpy' */
-static PyTypeObject *__pyx_ptype_5numpy_dtype = 0;
-static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0;
-static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0;
-static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0;
-static PyTypeObject *__pyx_ptype_5numpy_generic = 0;
-static PyTypeObject *__pyx_ptype_5numpy_number = 0;
-static PyTypeObject *__pyx_ptype_5numpy_integer = 0;
-static PyTypeObject *__pyx_ptype_5numpy_signedinteger = 0;
-static PyTypeObject *__pyx_ptype_5numpy_unsignedinteger = 0;
-static PyTypeObject *__pyx_ptype_5numpy_inexact = 0;
-static PyTypeObject *__pyx_ptype_5numpy_floating = 0;
-static PyTypeObject *__pyx_ptype_5numpy_complexfloating = 0;
-static PyTypeObject *__pyx_ptype_5numpy_flexible = 0;
-static PyTypeObject *__pyx_ptype_5numpy_character = 0;
-static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0;
-
-/* Module declarations from 'cython' */
-
-/* Module declarations from 'src.screening.gap_rqtest' */
-static PyTypeObject *__pyx_ptype_3src_9screening_10gap_rqtest_GAP_RQtest = 0;
-static __Pyx_TypeInfo __Pyx_TypeInfo_nn_npy_double = { "npy_double", NULL, sizeof(npy_double), { 0 }, 0, 'R', 0, 0 };
-static __Pyx_TypeInfo __Pyx_TypeInfo_long = { "long", NULL, sizeof(long), { 0 }, 0, IS_UNSIGNED(long) ? 'U' : 'I', IS_UNSIGNED(long), 0 };
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-#define __Pyx_MODULE_NAME "src.screening.gap_rqtest"
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-static PyObject *__pyx_builtin_TypeError;
-static PyObject *__pyx_builtin_ImportError;
-static const char __pyx_k_np[] = "np";
-static const char __pyx_k_gap[] = "gap";
-static const char __pyx_k_lbd[] = "lbd";
-static const char __pyx_k_main[] = "__main__";
-static const char __pyx_k_name[] = "__name__";
-static const char __pyx_k_ones[] = "ones";
-static const char __pyx_k_sqrt[] = "sqrt";
-static const char __pyx_k_test[] = "__test__";
-static const char __pyx_k_dtype[] = "dtype";
-static const char __pyx_k_index[] = "index";
-static const char __pyx_k_numpy[] = "numpy";
-static const char __pyx_k_range[] = "range";
-static const char __pyx_k_zeros[] = "zeros";
-static const char __pyx_k_Atcabs[] = "Atcabs";
-static const char __pyx_k_cumsum[] = "cumsum";
-static const char __pyx_k_double[] = "double";
-static const char __pyx_k_import[] = "__import__";
-static const char __pyx_k_reduce[] = "__reduce__";
-static const char __pyx_k_vec_rq[] = "vec_rq";
-static const char __pyx_k_argsort[] = "argsort";
-static const char __pyx_k_getstate[] = "__getstate__";
-static const char __pyx_k_setstate[] = "__setstate__";
-static const char __pyx_k_TypeError[] = "TypeError";
-static const char __pyx_k_reduce_ex[] = "__reduce_ex__";
-static const char __pyx_k_GAP_RQtest[] = "GAP_RQtest";
-static const char __pyx_k_vec_gammas[] = "vec_gammas";
-static const char __pyx_k_ImportError[] = "ImportError";
-static const char __pyx_k_offset_radius[] = "offset_radius";
-static const char __pyx_k_p_test_cython[] = "p-test cython";
-static const char __pyx_k_reduce_cython[] = "__reduce_cython__";
-static const char __pyx_k_setstate_cython[] = "__setstate_cython__";
-static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback";
-static const char __pyx_k_AbstractGapScreening[] = "AbstractGapScreening";
-static const char __pyx_k_src_screening_ascreening[] = "src.screening.ascreening";
-static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import";
-static const char __pyx_k_self_vec_cumsum_gammas_self_vec[] = "self.vec_cumsum_gammas,self.vec_rq cannot be converted to a Python object for pickling";
-static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import";
-static PyObject *__pyx_n_s_AbstractGapScreening;
-static PyObject *__pyx_n_s_Atcabs;
-static PyObject *__pyx_n_s_GAP_RQtest;
-static PyObject *__pyx_n_s_ImportError;
-static PyObject *__pyx_n_s_TypeError;
-static PyObject *__pyx_n_s_argsort;
-static PyObject *__pyx_n_s_cline_in_traceback;
-static PyObject *__pyx_n_s_cumsum;
-static PyObject *__pyx_n_s_double;
-static PyObject *__pyx_n_s_dtype;
-static PyObject *__pyx_n_s_gap;
-static PyObject *__pyx_n_s_getstate;
-static PyObject *__pyx_n_s_import;
-static PyObject *__pyx_n_s_index;
-static PyObject *__pyx_n_s_lbd;
-static PyObject *__pyx_n_s_main;
-static PyObject *__pyx_n_s_name;
-static PyObject *__pyx_n_s_np;
-static PyObject *__pyx_n_s_numpy;
-static PyObject *__pyx_kp_s_numpy_core_multiarray_failed_to;
-static PyObject *__pyx_kp_s_numpy_core_umath_failed_to_impor;
-static PyObject *__pyx_n_s_offset_radius;
-static PyObject *__pyx_n_s_ones;
-static PyObject *__pyx_kp_s_p_test_cython;
-static PyObject *__pyx_n_s_range;
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- return -1;
- }
- for (i = 0; i < ctx->head->field->type->ndim; i++) {
- arraysize *= ctx->head->field->type->arraysize[i];
- }
- ctx->is_valid_array = 0;
- ctx->enc_count = 1;
- }
- group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex);
- do {
- __Pyx_StructField* field = ctx->head->field;
- __Pyx_TypeInfo* type = field->type;
- if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') {
- size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex);
- } else {
- size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex);
- }
- if (ctx->enc_packmode == '@') {
- size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex);
- size_t align_mod_offset;
- if (align_at == 0) return -1;
- align_mod_offset = ctx->fmt_offset % align_at;
- if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset;
- if (ctx->struct_alignment == 0)
- ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type,
- ctx->is_complex);
- }
- if (type->size != size || type->typegroup != group) {
- if (type->typegroup == 'C' && type->fields != NULL) {
- size_t parent_offset = ctx->head->parent_offset + field->offset;
- ++ctx->head;
- ctx->head->field = type->fields;
- ctx->head->parent_offset = parent_offset;
- continue;
- }
- if ((type->typegroup == 'H' || group == 'H') && type->size == size) {
- } else {
- __Pyx_BufFmt_RaiseExpected(ctx);
- return -1;
- }
- }
- offset = ctx->head->parent_offset + field->offset;
- if (ctx->fmt_offset != offset) {
- PyErr_Format(PyExc_ValueError,
- "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected",
- (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset);
- return -1;
- }
- ctx->fmt_offset += size;
- if (arraysize)
- ctx->fmt_offset += (arraysize - 1) * size;
- --ctx->enc_count;
- while (1) {
- if (field == &ctx->root) {
- ctx->head = NULL;
- if (ctx->enc_count != 0) {
- __Pyx_BufFmt_RaiseExpected(ctx);
- return -1;
- }
- break;
- }
- ctx->head->field = ++field;
- if (field->type == NULL) {
- --ctx->head;
- field = ctx->head->field;
- continue;
- } else if (field->type->typegroup == 'S') {
- size_t parent_offset = ctx->head->parent_offset + field->offset;
- if (field->type->fields->type == NULL) continue;
- field = field->type->fields;
- ++ctx->head;
- ctx->head->field = field;
- ctx->head->parent_offset = parent_offset;
- break;
- } else {
- break;
- }
- }
- } while (ctx->enc_count);
- ctx->enc_type = 0;
- ctx->is_complex = 0;
- return 0;
-}
-static PyObject *
-__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp)
-{
- const char *ts = *tsp;
- int i = 0, number, ndim;
- ++ts;
- if (ctx->new_count != 1) {
- PyErr_SetString(PyExc_ValueError,
- "Cannot handle repeated arrays in format string");
- return NULL;
- }
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ndim = ctx->head->field->type->ndim;
- while (*ts && *ts != ')') {
- switch (*ts) {
- case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue;
- default: break;
- }
- number = __Pyx_BufFmt_ExpectNumber(&ts);
- if (number == -1) return NULL;
- if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i])
- return PyErr_Format(PyExc_ValueError,
- "Expected a dimension of size %zu, got %d",
- ctx->head->field->type->arraysize[i], number);
- if (*ts != ',' && *ts != ')')
- return PyErr_Format(PyExc_ValueError,
- "Expected a comma in format string, got '%c'", *ts);
- if (*ts == ',') ts++;
- i++;
- }
- if (i != ndim)
- return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d",
- ctx->head->field->type->ndim, i);
- if (!*ts) {
- PyErr_SetString(PyExc_ValueError,
- "Unexpected end of format string, expected ')'");
- return NULL;
- }
- ctx->is_valid_array = 1;
- ctx->new_count = 1;
- *tsp = ++ts;
- return Py_None;
-}
-static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) {
- int got_Z = 0;
- while (1) {
- switch(*ts) {
- case 0:
- if (ctx->enc_type != 0 && ctx->head == NULL) {
- __Pyx_BufFmt_RaiseExpected(ctx);
- return NULL;
- }
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- if (ctx->head != NULL) {
- __Pyx_BufFmt_RaiseExpected(ctx);
- return NULL;
- }
- return ts;
- case ' ':
- case '\r':
- case '\n':
- ++ts;
- break;
- case '<':
- if (!__Pyx_Is_Little_Endian()) {
- PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler");
- return NULL;
- }
- ctx->new_packmode = '=';
- ++ts;
- break;
- case '>':
- case '!':
- if (__Pyx_Is_Little_Endian()) {
- PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler");
- return NULL;
- }
- ctx->new_packmode = '=';
- ++ts;
- break;
- case '=':
- case '@':
- case '^':
- ctx->new_packmode = *ts++;
- break;
- case 'T':
- {
- const char* ts_after_sub;
- size_t i, struct_count = ctx->new_count;
- size_t struct_alignment = ctx->struct_alignment;
- ctx->new_count = 1;
- ++ts;
- if (*ts != '{') {
- PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'");
- return NULL;
- }
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->enc_type = 0;
- ctx->enc_count = 0;
- ctx->struct_alignment = 0;
- ++ts;
- ts_after_sub = ts;
- for (i = 0; i != struct_count; ++i) {
- ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts);
- if (!ts_after_sub) return NULL;
- }
- ts = ts_after_sub;
- if (struct_alignment) ctx->struct_alignment = struct_alignment;
- }
- break;
- case '}':
- {
- size_t alignment = ctx->struct_alignment;
- ++ts;
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->enc_type = 0;
- if (alignment && ctx->fmt_offset % alignment) {
- ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment);
- }
- }
- return ts;
- case 'x':
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->fmt_offset += ctx->new_count;
- ctx->new_count = 1;
- ctx->enc_count = 0;
- ctx->enc_type = 0;
- ctx->enc_packmode = ctx->new_packmode;
- ++ts;
- break;
- case 'Z':
- got_Z = 1;
- ++ts;
- if (*ts != 'f' && *ts != 'd' && *ts != 'g') {
- __Pyx_BufFmt_RaiseUnexpectedChar('Z');
- return NULL;
- }
- CYTHON_FALLTHROUGH;
- case '?': case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I':
- case 'l': case 'L': case 'q': case 'Q':
- case 'f': case 'd': case 'g':
- case 'O': case 'p':
- if ((ctx->enc_type == *ts) && (got_Z == ctx->is_complex) &&
- (ctx->enc_packmode == ctx->new_packmode) && (!ctx->is_valid_array)) {
- ctx->enc_count += ctx->new_count;
- ctx->new_count = 1;
- got_Z = 0;
- ++ts;
- break;
- }
- CYTHON_FALLTHROUGH;
- case 's':
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->enc_count = ctx->new_count;
- ctx->enc_packmode = ctx->new_packmode;
- ctx->enc_type = *ts;
- ctx->is_complex = got_Z;
- ++ts;
- ctx->new_count = 1;
- got_Z = 0;
- break;
- case ':':
- ++ts;
- while(*ts != ':') ++ts;
- ++ts;
- break;
- case '(':
- if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL;
- break;
- default:
- {
- int number = __Pyx_BufFmt_ExpectNumber(&ts);
- if (number == -1) return NULL;
- ctx->new_count = (size_t)number;
- }
- }
- }
-}
-
-/* BufferGetAndValidate */
- static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) {
- if (unlikely(info->buf == NULL)) return;
- if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL;
- __Pyx_ReleaseBuffer(info);
-}
-static void __Pyx_ZeroBuffer(Py_buffer* buf) {
- buf->buf = NULL;
- buf->obj = NULL;
- buf->strides = __Pyx_zeros;
- buf->shape = __Pyx_zeros;
- buf->suboffsets = __Pyx_minusones;
-}
-static int __Pyx__GetBufferAndValidate(
- Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags,
- int nd, int cast, __Pyx_BufFmt_StackElem* stack)
-{
- buf->buf = NULL;
- if (unlikely(__Pyx_GetBuffer(obj, buf, flags) == -1)) {
- __Pyx_ZeroBuffer(buf);
- return -1;
- }
- if (unlikely(buf->ndim != nd)) {
- PyErr_Format(PyExc_ValueError,
- "Buffer has wrong number of dimensions (expected %d, got %d)",
- nd, buf->ndim);
- goto fail;
- }
- if (!cast) {
- __Pyx_BufFmt_Context ctx;
- __Pyx_BufFmt_Init(&ctx, stack, dtype);
- if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail;
- }
- if (unlikely((size_t)buf->itemsize != dtype->size)) {
- PyErr_Format(PyExc_ValueError,
- "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)",
- buf->itemsize, (buf->itemsize > 1) ? "s" : "",
- dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : "");
- goto fail;
- }
- if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones;
- return 0;
-fail:;
- __Pyx_SafeReleaseBuffer(buf);
- return -1;
-}
-
-/* PyErrFetchRestore */
- #if CYTHON_FAST_THREAD_STATE
-static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) {
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- tmp_type = tstate->curexc_type;
- tmp_value = tstate->curexc_value;
- tmp_tb = tstate->curexc_traceback;
- tstate->curexc_type = type;
- tstate->curexc_value = value;
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-}
-static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) {
- *type = tstate->curexc_type;
- *value = tstate->curexc_value;
- *tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-}
-#endif
-
-/* PyDictVersioning */
- #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS
-static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj) {
- PyObject *dict = Py_TYPE(obj)->tp_dict;
- return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0;
-}
-static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj) {
- PyObject **dictptr = NULL;
- Py_ssize_t offset = Py_TYPE(obj)->tp_dictoffset;
- if (offset) {
-#if CYTHON_COMPILING_IN_CPYTHON
- dictptr = (likely(offset > 0)) ? (PyObject **) ((char *)obj + offset) : _PyObject_GetDictPtr(obj);
-#else
- dictptr = _PyObject_GetDictPtr(obj);
-#endif
- }
- return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0;
-}
-static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version) {
- PyObject *dict = Py_TYPE(obj)->tp_dict;
- if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict)))
- return 0;
- return obj_dict_version == __Pyx_get_object_dict_version(obj);
-}
-#endif
-
-/* GetModuleGlobalName */
- #if CYTHON_USE_DICT_VERSIONS
-static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value)
-#else
-static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name)
-#endif
-{
- PyObject *result;
-#if !CYTHON_AVOID_BORROWED_REFS
-#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1
- result = _PyDict_GetItem_KnownHash(__pyx_d, name, ((PyASCIIObject *) name)->hash);
- __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version)
- if (likely(result)) {
- return __Pyx_NewRef(result);
- } else if (unlikely(PyErr_Occurred())) {
- return NULL;
- }
-#else
- result = PyDict_GetItem(__pyx_d, name);
- __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version)
- if (likely(result)) {
- return __Pyx_NewRef(result);
- }
-#endif
-#else
- result = PyObject_GetItem(__pyx_d, name);
- __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version)
- if (likely(result)) {
- return __Pyx_NewRef(result);
- }
- PyErr_Clear();
-#endif
- return __Pyx_GetBuiltinName(name);
-}
-
-/* PyCFunctionFastCall */
- #if CYTHON_FAST_PYCCALL
-static CYTHON_INLINE PyObject * __Pyx_PyCFunction_FastCall(PyObject *func_obj, PyObject **args, Py_ssize_t nargs) {
- PyCFunctionObject *func = (PyCFunctionObject*)func_obj;
- PyCFunction meth = PyCFunction_GET_FUNCTION(func);
- PyObject *self = PyCFunction_GET_SELF(func);
- int flags = PyCFunction_GET_FLAGS(func);
- assert(PyCFunction_Check(func));
- assert(METH_FASTCALL == (flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS)));
- assert(nargs >= 0);
- assert(nargs == 0 || args != NULL);
- /* _PyCFunction_FastCallDict() must not be called with an exception set,
- because it may clear it (directly or indirectly) and so the
- caller loses its exception */
- assert(!PyErr_Occurred());
- if ((PY_VERSION_HEX < 0x030700A0) || unlikely(flags & METH_KEYWORDS)) {
- return (*((__Pyx_PyCFunctionFastWithKeywords)(void*)meth)) (self, args, nargs, NULL);
- } else {
- return (*((__Pyx_PyCFunctionFast)(void*)meth)) (self, args, nargs);
- }
-}
-#endif
-
-/* PyFunctionFastCall */
- #if CYTHON_FAST_PYCALL
-static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args, Py_ssize_t na,
- PyObject *globals) {
- PyFrameObject *f;
- PyThreadState *tstate = __Pyx_PyThreadState_Current;
- PyObject **fastlocals;
- Py_ssize_t i;
- PyObject *result;
- assert(globals != NULL);
- /* XXX Perhaps we should create a specialized
- PyFrame_New() that doesn't take locals, but does
- take builtins without sanity checking them.
- */
- assert(tstate != NULL);
- f = PyFrame_New(tstate, co, globals, NULL);
- if (f == NULL) {
- return NULL;
- }
- fastlocals = __Pyx_PyFrame_GetLocalsplus(f);
- for (i = 0; i < na; i++) {
- Py_INCREF(*args);
- fastlocals[i] = *args++;
- }
- result = PyEval_EvalFrameEx(f,0);
- ++tstate->recursion_depth;
- Py_DECREF(f);
- --tstate->recursion_depth;
- return result;
-}
-#if 1 || PY_VERSION_HEX < 0x030600B1
-static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs) {
- PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func);
- PyObject *globals = PyFunction_GET_GLOBALS(func);
- PyObject *argdefs = PyFunction_GET_DEFAULTS(func);
- PyObject *closure;
-#if PY_MAJOR_VERSION >= 3
- PyObject *kwdefs;
-#endif
- PyObject *kwtuple, **k;
- PyObject **d;
- Py_ssize_t nd;
- Py_ssize_t nk;
- PyObject *result;
- assert(kwargs == NULL || PyDict_Check(kwargs));
- nk = kwargs ? PyDict_Size(kwargs) : 0;
- if (Py_EnterRecursiveCall((char*)" while calling a Python object")) {
- return NULL;
- }
- if (
-#if PY_MAJOR_VERSION >= 3
- co->co_kwonlyargcount == 0 &&
-#endif
- likely(kwargs == NULL || nk == 0) &&
- co->co_flags == (CO_OPTIMIZED | CO_NEWLOCALS | CO_NOFREE)) {
- if (argdefs == NULL && co->co_argcount == nargs) {
- result = __Pyx_PyFunction_FastCallNoKw(co, args, nargs, globals);
- goto done;
- }
- else if (nargs == 0 && argdefs != NULL
- && co->co_argcount == Py_SIZE(argdefs)) {
- /* function called with no arguments, but all parameters have
- a default value: use default values as arguments .*/
- args = &PyTuple_GET_ITEM(argdefs, 0);
- result =__Pyx_PyFunction_FastCallNoKw(co, args, Py_SIZE(argdefs), globals);
- goto done;
- }
- }
- if (kwargs != NULL) {
- Py_ssize_t pos, i;
- kwtuple = PyTuple_New(2 * nk);
- if (kwtuple == NULL) {
- result = NULL;
- goto done;
- }
- k = &PyTuple_GET_ITEM(kwtuple, 0);
- pos = i = 0;
- while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) {
- Py_INCREF(k[i]);
- Py_INCREF(k[i+1]);
- i += 2;
- }
- nk = i / 2;
- }
- else {
- kwtuple = NULL;
- k = NULL;
- }
- closure = PyFunction_GET_CLOSURE(func);
-#if PY_MAJOR_VERSION >= 3
- kwdefs = PyFunction_GET_KW_DEFAULTS(func);
-#endif
- if (argdefs != NULL) {
- d = &PyTuple_GET_ITEM(argdefs, 0);
- nd = Py_SIZE(argdefs);
- }
- else {
- d = NULL;
- nd = 0;
- }
-#if PY_MAJOR_VERSION >= 3
- result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL,
- args, (int)nargs,
- k, (int)nk,
- d, (int)nd, kwdefs, closure);
-#else
- result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL,
- args, (int)nargs,
- k, (int)nk,
- d, (int)nd, closure);
-#endif
- Py_XDECREF(kwtuple);
-done:
- Py_LeaveRecursiveCall();
- return result;
-}
-#endif
-#endif
-
-/* PyObjectCall */
- #if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) {
- PyObject *result;
- ternaryfunc call = Py_TYPE(func)->tp_call;
- if (unlikely(!call))
- return PyObject_Call(func, arg, kw);
- if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
- return NULL;
- result = (*call)(func, arg, kw);
- Py_LeaveRecursiveCall();
- if (unlikely(!result) && unlikely(!PyErr_Occurred())) {
- PyErr_SetString(
- PyExc_SystemError,
- "NULL result without error in PyObject_Call");
- }
- return result;
-}
-#endif
-
-/* PyObjectCall2Args */
- static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2) {
- PyObject *args, *result = NULL;
- #if CYTHON_FAST_PYCALL
- if (PyFunction_Check(function)) {
- PyObject *args[2] = {arg1, arg2};
- return __Pyx_PyFunction_FastCall(function, args, 2);
- }
- #endif
- #if CYTHON_FAST_PYCCALL
- if (__Pyx_PyFastCFunction_Check(function)) {
- PyObject *args[2] = {arg1, arg2};
- return __Pyx_PyCFunction_FastCall(function, args, 2);
- }
- #endif
- args = PyTuple_New(2);
- if (unlikely(!args)) goto done;
- Py_INCREF(arg1);
- PyTuple_SET_ITEM(args, 0, arg1);
- Py_INCREF(arg2);
- PyTuple_SET_ITEM(args, 1, arg2);
- Py_INCREF(function);
- result = __Pyx_PyObject_Call(function, args, NULL);
- Py_DECREF(args);
- Py_DECREF(function);
-done:
- return result;
-}
-
-/* PyObjectCallMethO */
- #if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) {
- PyObject *self, *result;
- PyCFunction cfunc;
- cfunc = PyCFunction_GET_FUNCTION(func);
- self = PyCFunction_GET_SELF(func);
- if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
- return NULL;
- result = cfunc(self, arg);
- Py_LeaveRecursiveCall();
- if (unlikely(!result) && unlikely(!PyErr_Occurred())) {
- PyErr_SetString(
- PyExc_SystemError,
- "NULL result without error in PyObject_Call");
- }
- return result;
-}
-#endif
-
-/* PyObjectCallOneArg */
- #if CYTHON_COMPILING_IN_CPYTHON
-static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) {
- PyObject *result;
- PyObject *args = PyTuple_New(1);
- if (unlikely(!args)) return NULL;
- Py_INCREF(arg);
- PyTuple_SET_ITEM(args, 0, arg);
- result = __Pyx_PyObject_Call(func, args, NULL);
- Py_DECREF(args);
- return result;
-}
-static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
-#if CYTHON_FAST_PYCALL
- if (PyFunction_Check(func)) {
- return __Pyx_PyFunction_FastCall(func, &arg, 1);
- }
-#endif
- if (likely(PyCFunction_Check(func))) {
- if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) {
- return __Pyx_PyObject_CallMethO(func, arg);
-#if CYTHON_FAST_PYCCALL
- } else if (__Pyx_PyFastCFunction_Check(func)) {
- return __Pyx_PyCFunction_FastCall(func, &arg, 1);
-#endif
- }
- }
- return __Pyx__PyObject_CallOneArg(func, arg);
-}
-#else
-static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
- PyObject *result;
- PyObject *args = PyTuple_Pack(1, arg);
- if (unlikely(!args)) return NULL;
- result = __Pyx_PyObject_Call(func, args, NULL);
- Py_DECREF(args);
- return result;
-}
-#endif
-
-/* ExtTypeTest */
- static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
- if (unlikely(!type)) {
- PyErr_SetString(PyExc_SystemError, "Missing type object");
- return 0;
- }
- if (likely(__Pyx_TypeCheck(obj, type)))
- return 1;
- PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s",
- Py_TYPE(obj)->tp_name, type->tp_name);
- return 0;
-}
-
-/* BufferFallbackError */
- static void __Pyx_RaiseBufferFallbackError(void) {
- PyErr_SetString(PyExc_ValueError,
- "Buffer acquisition failed on assignment; and then reacquiring the old buffer failed too!");
-}
-
-/* GetItemInt */
- static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
- PyObject *r;
- if (!j) return NULL;
- r = PyObject_GetItem(o, j);
- Py_DECREF(j);
- return r;
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
- CYTHON_NCP_UNUSED int wraparound,
- CYTHON_NCP_UNUSED int boundscheck) {
-#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
- Py_ssize_t wrapped_i = i;
- if (wraparound & unlikely(i < 0)) {
- wrapped_i += PyList_GET_SIZE(o);
- }
- if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, wrapped_i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
- CYTHON_NCP_UNUSED int wraparound,
- CYTHON_NCP_UNUSED int boundscheck) {
-#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
- Py_ssize_t wrapped_i = i;
- if (wraparound & unlikely(i < 0)) {
- wrapped_i += PyTuple_GET_SIZE(o);
- }
- if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, wrapped_i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list,
- CYTHON_NCP_UNUSED int wraparound,
- CYTHON_NCP_UNUSED int boundscheck) {
-#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS
- if (is_list || PyList_CheckExact(o)) {
- Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
- if ((!boundscheck) || (likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o))))) {
- PyObject *r = PyList_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- }
- else if (PyTuple_CheckExact(o)) {
- Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
- if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- } else {
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_item)) {
- if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (likely(l >= 0)) {
- i += l;
- } else {
- if (!PyErr_ExceptionMatches(PyExc_OverflowError))
- return NULL;
- PyErr_Clear();
- }
- }
- return m->sq_item(o, i);
- }
- }
-#else
- if (is_list || PySequence_Check(o)) {
- return PySequence_GetItem(o, i);
- }
-#endif
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-}
-
-/* ObjectGetItem */
- #if CYTHON_USE_TYPE_SLOTS
-static PyObject *__Pyx_PyObject_GetIndex(PyObject *obj, PyObject* index) {
- PyObject *runerr;
- Py_ssize_t key_value;
- PySequenceMethods *m = Py_TYPE(obj)->tp_as_sequence;
- if (unlikely(!(m && m->sq_item))) {
- PyErr_Format(PyExc_TypeError, "'%.200s' object is not subscriptable", Py_TYPE(obj)->tp_name);
- return NULL;
- }
- key_value = __Pyx_PyIndex_AsSsize_t(index);
- if (likely(key_value != -1 || !(runerr = PyErr_Occurred()))) {
- return __Pyx_GetItemInt_Fast(obj, key_value, 0, 1, 1);
- }
- if (PyErr_GivenExceptionMatches(runerr, PyExc_OverflowError)) {
- PyErr_Clear();
- PyErr_Format(PyExc_IndexError, "cannot fit '%.200s' into an index-sized integer", Py_TYPE(index)->tp_name);
- }
- return NULL;
-}
-static PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key) {
- PyMappingMethods *m = Py_TYPE(obj)->tp_as_mapping;
- if (likely(m && m->mp_subscript)) {
- return m->mp_subscript(obj, key);
- }
- return __Pyx_PyObject_GetIndex(obj, key);
-}
-#endif
-
-/* RaiseException */
- #if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
- CYTHON_UNUSED PyObject *cause) {
- __Pyx_PyThreadState_declare
- Py_XINCREF(type);
- if (!value || value == Py_None)
- value = NULL;
- else
- Py_INCREF(value);
- if (!tb || tb == Py_None)
- tb = NULL;
- else {
- Py_INCREF(tb);
- if (!PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- }
- if (PyType_Check(type)) {
-#if CYTHON_COMPILING_IN_PYPY
- if (!value) {
- Py_INCREF(Py_None);
- value = Py_None;
- }
-#endif
- PyErr_NormalizeException(&type, &value, &tb);
- } else {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto raise_error;
- }
- value = type;
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- }
- __Pyx_PyThreadState_assign
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-#else
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- PyObject* owned_instance = NULL;
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (PyExceptionClass_Check(type)) {
- PyObject *instance_class = NULL;
- if (value && PyExceptionInstance_Check(value)) {
- instance_class = (PyObject*) Py_TYPE(value);
- if (instance_class != type) {
- int is_subclass = PyObject_IsSubclass(instance_class, type);
- if (!is_subclass) {
- instance_class = NULL;
- } else if (unlikely(is_subclass == -1)) {
- goto bad;
- } else {
- type = instance_class;
- }
- }
- }
- if (!instance_class) {
- PyObject *args;
- if (!value)
- args = PyTuple_New(0);
- else if (PyTuple_Check(value)) {
- Py_INCREF(value);
- args = value;
- } else
- args = PyTuple_Pack(1, value);
- if (!args)
- goto bad;
- owned_instance = PyObject_Call(type, args, NULL);
- Py_DECREF(args);
- if (!owned_instance)
- goto bad;
- value = owned_instance;
- if (!PyExceptionInstance_Check(value)) {
- PyErr_Format(PyExc_TypeError,
- "calling %R should have returned an instance of "
- "BaseException, not %R",
- type, Py_TYPE(value));
- goto bad;
- }
- }
- } else {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto bad;
- }
- if (cause) {
- PyObject *fixed_cause;
- if (cause == Py_None) {
- fixed_cause = NULL;
- } else if (PyExceptionClass_Check(cause)) {
- fixed_cause = PyObject_CallObject(cause, NULL);
- if (fixed_cause == NULL)
- goto bad;
- } else if (PyExceptionInstance_Check(cause)) {
- fixed_cause = cause;
- Py_INCREF(fixed_cause);
- } else {
- PyErr_SetString(PyExc_TypeError,
- "exception causes must derive from "
- "BaseException");
- goto bad;
- }
- PyException_SetCause(value, fixed_cause);
- }
- PyErr_SetObject(type, value);
- if (tb) {
-#if CYTHON_COMPILING_IN_PYPY
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb);
- Py_INCREF(tb);
- PyErr_Restore(tmp_type, tmp_value, tb);
- Py_XDECREF(tmp_tb);
-#else
- PyThreadState *tstate = __Pyx_PyThreadState_Current;
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
-#endif
- }
-bad:
- Py_XDECREF(owned_instance);
- return;
-}
-#endif
-
-/* GetTopmostException */
- #if CYTHON_USE_EXC_INFO_STACK
-static _PyErr_StackItem *
-__Pyx_PyErr_GetTopmostException(PyThreadState *tstate)
-{
- _PyErr_StackItem *exc_info = tstate->exc_info;
- while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) &&
- exc_info->previous_item != NULL)
- {
- exc_info = exc_info->previous_item;
- }
- return exc_info;
-}
-#endif
-
-/* SaveResetException */
- #if CYTHON_FAST_THREAD_STATE
-static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) {
- #if CYTHON_USE_EXC_INFO_STACK
- _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate);
- *type = exc_info->exc_type;
- *value = exc_info->exc_value;
- *tb = exc_info->exc_traceback;
- #else
- *type = tstate->exc_type;
- *value = tstate->exc_value;
- *tb = tstate->exc_traceback;
- #endif
- Py_XINCREF(*type);
- Py_XINCREF(*value);
- Py_XINCREF(*tb);
-}
-static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) {
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- #if CYTHON_USE_EXC_INFO_STACK
- _PyErr_StackItem *exc_info = tstate->exc_info;
- tmp_type = exc_info->exc_type;
- tmp_value = exc_info->exc_value;
- tmp_tb = exc_info->exc_traceback;
- exc_info->exc_type = type;
- exc_info->exc_value = value;
- exc_info->exc_traceback = tb;
- #else
- tmp_type = tstate->exc_type;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = type;
- tstate->exc_value = value;
- tstate->exc_traceback = tb;
- #endif
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-}
-#endif
-
-/* PyErrExceptionMatches */
- #if CYTHON_FAST_THREAD_STATE
-static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) {
- Py_ssize_t i, n;
- n = PyTuple_GET_SIZE(tuple);
-#if PY_MAJOR_VERSION >= 3
- for (i=0; i<n; i++) {
- if (exc_type == PyTuple_GET_ITEM(tuple, i)) return 1;
- }
-#endif
- for (i=0; i<n; i++) {
- if (__Pyx_PyErr_GivenExceptionMatches(exc_type, PyTuple_GET_ITEM(tuple, i))) return 1;
- }
- return 0;
-}
-static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err) {
- PyObject *exc_type = tstate->curexc_type;
- if (exc_type == err) return 1;
- if (unlikely(!exc_type)) return 0;
- if (unlikely(PyTuple_Check(err)))
- return __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err);
- return __Pyx_PyErr_GivenExceptionMatches(exc_type, err);
-}
-#endif
-
-/* GetException */
- #if CYTHON_FAST_THREAD_STATE
-static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb)
-#else
-static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
-#endif
-{
- PyObject *local_type, *local_value, *local_tb;
-#if CYTHON_FAST_THREAD_STATE
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- local_type = tstate->curexc_type;
- local_value = tstate->curexc_value;
- local_tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(&local_type, &local_value, &local_tb);
-#endif
- PyErr_NormalizeException(&local_type, &local_value, &local_tb);
-#if CYTHON_FAST_THREAD_STATE
- if (unlikely(tstate->curexc_type))
-#else
- if (unlikely(PyErr_Occurred()))
-#endif
- goto bad;
- #if PY_MAJOR_VERSION >= 3
- if (local_tb) {
- if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
- goto bad;
- }
- #endif
- Py_XINCREF(local_tb);
- Py_XINCREF(local_type);
- Py_XINCREF(local_value);
- *type = local_type;
- *value = local_value;
- *tb = local_tb;
-#if CYTHON_FAST_THREAD_STATE
- #if CYTHON_USE_EXC_INFO_STACK
- {
- _PyErr_StackItem *exc_info = tstate->exc_info;
- tmp_type = exc_info->exc_type;
- tmp_value = exc_info->exc_value;
- tmp_tb = exc_info->exc_traceback;
- exc_info->exc_type = local_type;
- exc_info->exc_value = local_value;
- exc_info->exc_traceback = local_tb;
- }
- #else
- tmp_type = tstate->exc_type;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = local_type;
- tstate->exc_value = local_value;
- tstate->exc_traceback = local_tb;
- #endif
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(local_type, local_value, local_tb);
-#endif
- return 0;
-bad:
- *type = 0;
- *value = 0;
- *tb = 0;
- Py_XDECREF(local_type);
- Py_XDECREF(local_value);
- Py_XDECREF(local_tb);
- return -1;
-}
-
-/* PyObject_GenericGetAttrNoDict */
- #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000
-static PyObject *__Pyx_RaiseGenericGetAttributeError(PyTypeObject *tp, PyObject *attr_name) {
- PyErr_Format(PyExc_AttributeError,
-#if PY_MAJOR_VERSION >= 3
- "'%.50s' object has no attribute '%U'",
- tp->tp_name, attr_name);
-#else
- "'%.50s' object has no attribute '%.400s'",
- tp->tp_name, PyString_AS_STRING(attr_name));
-#endif
- return NULL;
-}
-static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name) {
- PyObject *descr;
- PyTypeObject *tp = Py_TYPE(obj);
- if (unlikely(!PyString_Check(attr_name))) {
- return PyObject_GenericGetAttr(obj, attr_name);
- }
- assert(!tp->tp_dictoffset);
- descr = _PyType_Lookup(tp, attr_name);
- if (unlikely(!descr)) {
- return __Pyx_RaiseGenericGetAttributeError(tp, attr_name);
- }
- Py_INCREF(descr);
- #if PY_MAJOR_VERSION < 3
- if (likely(PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_HAVE_CLASS)))
- #endif
- {
- descrgetfunc f = Py_TYPE(descr)->tp_descr_get;
- if (unlikely(f)) {
- PyObject *res = f(descr, obj, (PyObject *)tp);
- Py_DECREF(descr);
- return res;
- }
- }
- return descr;
-}
-#endif
-
-/* PyObject_GenericGetAttr */
- #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000
-static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name) {
- if (unlikely(Py_TYPE(obj)->tp_dictoffset)) {
- return PyObject_GenericGetAttr(obj, attr_name);
- }
- return __Pyx_PyObject_GenericGetAttrNoDict(obj, attr_name);
-}
-#endif
-
-/* PyObjectGetAttrStrNoError */
- static void __Pyx_PyObject_GetAttrStr_ClearAttributeError(void) {
- __Pyx_PyThreadState_declare
- __Pyx_PyThreadState_assign
- if (likely(__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError)))
- __Pyx_PyErr_Clear();
-}
-static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name) {
- PyObject *result;
-#if CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_TYPE_SLOTS && PY_VERSION_HEX >= 0x030700B1
- PyTypeObject* tp = Py_TYPE(obj);
- if (likely(tp->tp_getattro == PyObject_GenericGetAttr)) {
- return _PyObject_GenericGetAttrWithDict(obj, attr_name, NULL, 1);
- }
-#endif
- result = __Pyx_PyObject_GetAttrStr(obj, attr_name);
- if (unlikely(!result)) {
- __Pyx_PyObject_GetAttrStr_ClearAttributeError();
- }
- return result;
-}
-
-/* SetupReduce */
- static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) {
- int ret;
- PyObject *name_attr;
- name_attr = __Pyx_PyObject_GetAttrStr(meth, __pyx_n_s_name);
- if (likely(name_attr)) {
- ret = PyObject_RichCompareBool(name_attr, name, Py_EQ);
- } else {
- ret = -1;
- }
- if (unlikely(ret < 0)) {
- PyErr_Clear();
- ret = 0;
- }
- Py_XDECREF(name_attr);
- return ret;
-}
-static int __Pyx_setup_reduce(PyObject* type_obj) {
- int ret = 0;
- PyObject *object_reduce = NULL;
- PyObject *object_reduce_ex = NULL;
- PyObject *reduce = NULL;
- PyObject *reduce_ex = NULL;
- PyObject *reduce_cython = NULL;
- PyObject *setstate = NULL;
- PyObject *setstate_cython = NULL;
-#if CYTHON_USE_PYTYPE_LOOKUP
- if (_PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate)) goto __PYX_GOOD;
-#else
- if (PyObject_HasAttr(type_obj, __pyx_n_s_getstate)) goto __PYX_GOOD;
-#endif
-#if CYTHON_USE_PYTYPE_LOOKUP
- object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD;
-#else
- object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD;
-#endif
- reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto __PYX_BAD;
- if (reduce_ex == object_reduce_ex) {
-#if CYTHON_USE_PYTYPE_LOOKUP
- object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD;
-#else
- object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD;
-#endif
- reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto __PYX_BAD;
- if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) {
- reduce_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_reduce_cython);
- if (likely(reduce_cython)) {
- ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD;
- ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD;
- } else if (reduce == object_reduce || PyErr_Occurred()) {
- goto __PYX_BAD;
- }
- setstate = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate);
- if (!setstate) PyErr_Clear();
- if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) {
- setstate_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_setstate_cython);
- if (likely(setstate_cython)) {
- ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD;
- ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD;
- } else if (!setstate || PyErr_Occurred()) {
- goto __PYX_BAD;
- }
- }
- PyType_Modified((PyTypeObject*)type_obj);
- }
- }
- goto __PYX_GOOD;
-__PYX_BAD:
- if (!PyErr_Occurred())
- PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name);
- ret = -1;
-__PYX_GOOD:
-#if !CYTHON_USE_PYTYPE_LOOKUP
- Py_XDECREF(object_reduce);
- Py_XDECREF(object_reduce_ex);
-#endif
- Py_XDECREF(reduce);
- Py_XDECREF(reduce_ex);
- Py_XDECREF(reduce_cython);
- Py_XDECREF(setstate);
- Py_XDECREF(setstate_cython);
- return ret;
-}
-
-/* TypeImport */
- #ifndef __PYX_HAVE_RT_ImportType
-#define __PYX_HAVE_RT_ImportType
-static PyTypeObject *__Pyx_ImportType(PyObject *module, const char *module_name, const char *class_name,
- size_t size, enum __Pyx_ImportType_CheckSize check_size)
-{
- PyObject *result = 0;
- char warning[200];
- Py_ssize_t basicsize;
-#ifdef Py_LIMITED_API
- PyObject *py_basicsize;
-#endif
- result = PyObject_GetAttrString(module, class_name);
- if (!result)
- goto bad;
- if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
- "%.200s.%.200s is not a type object",
- module_name, class_name);
- goto bad;
- }
-#ifndef Py_LIMITED_API
- basicsize = ((PyTypeObject *)result)->tp_basicsize;
-#else
- py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
- if (!py_basicsize)
- goto bad;
- basicsize = PyLong_AsSsize_t(py_basicsize);
- Py_DECREF(py_basicsize);
- py_basicsize = 0;
- if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
- goto bad;
-#endif
- if ((size_t)basicsize < size) {
- PyErr_Format(PyExc_ValueError,
- "%.200s.%.200s size changed, may indicate binary incompatibility. "
- "Expected %zd from C header, got %zd from PyObject",
- module_name, class_name, size, basicsize);
- goto bad;
- }
- if (check_size == __Pyx_ImportType_CheckSize_Error && (size_t)basicsize != size) {
- PyErr_Format(PyExc_ValueError,
- "%.200s.%.200s size changed, may indicate binary incompatibility. "
- "Expected %zd from C header, got %zd from PyObject",
- module_name, class_name, size, basicsize);
- goto bad;
- }
- else if (check_size == __Pyx_ImportType_CheckSize_Warn && (size_t)basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
- "%s.%s size changed, may indicate binary incompatibility. "
- "Expected %zd from C header, got %zd from PyObject",
- module_name, class_name, size, basicsize);
- if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
- }
- return (PyTypeObject *)result;
-bad:
- Py_XDECREF(result);
- return NULL;
-}
-#endif
-
-/* Import */
- static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- #if PY_MAJOR_VERSION < 3
- PyObject *py_import;
- py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
- if (!py_import)
- goto bad;
- #endif
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
- }
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- {
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if ((1) && (strchr(__Pyx_MODULE_NAME, '.'))) {
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, 1);
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0;
- }
- #endif
- if (!module) {
- #if PY_MAJOR_VERSION < 3
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, (PyObject *)NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, level);
- #endif
- }
- }
-bad:
- #if PY_MAJOR_VERSION < 3
- Py_XDECREF(py_import);
- #endif
- Py_XDECREF(empty_list);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-/* ImportFrom */
- static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) {
- PyObject* value = __Pyx_PyObject_GetAttrStr(module, name);
- if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) {
- PyErr_Format(PyExc_ImportError,
- #if PY_MAJOR_VERSION < 3
- "cannot import name %.230s", PyString_AS_STRING(name));
- #else
- "cannot import name %S", name);
- #endif
- }
- return value;
-}
-
-/* CLineInTraceback */
- #ifndef CYTHON_CLINE_IN_TRACEBACK
-static int __Pyx_CLineForTraceback(CYTHON_NCP_UNUSED PyThreadState *tstate, int c_line) {
- PyObject *use_cline;
- PyObject *ptype, *pvalue, *ptraceback;
-#if CYTHON_COMPILING_IN_CPYTHON
- PyObject **cython_runtime_dict;
-#endif
- if (unlikely(!__pyx_cython_runtime)) {
- return c_line;
- }
- __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback);
-#if CYTHON_COMPILING_IN_CPYTHON
- cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime);
- if (likely(cython_runtime_dict)) {
- __PYX_PY_DICT_LOOKUP_IF_MODIFIED(
- use_cline, *cython_runtime_dict,
- __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback))
- } else
-#endif
- {
- PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback);
- if (use_cline_obj) {
- use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True;
- Py_DECREF(use_cline_obj);
- } else {
- PyErr_Clear();
- use_cline = NULL;
- }
- }
- if (!use_cline) {
- c_line = 0;
- PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False);
- }
- else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) {
- c_line = 0;
- }
- __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback);
- return c_line;
-}
-#endif
-
-/* CodeObjectCache */
- static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = start + (end - start) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-/* AddTraceback */
- #include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0,
- 0,
- 0,
- 0,
- 0,
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line,
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyFrameObject *py_frame = 0;
- PyThreadState *tstate = __Pyx_PyThreadState_Current;
- if (c_line) {
- c_line = __Pyx_CLineForTraceback(tstate, c_line);
- }
- py_code = __pyx_find_code_object(c_line ? -c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? -c_line : py_line, py_code);
- }
- py_frame = PyFrame_New(
- tstate, /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- __pyx_d, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- __Pyx_PyFrame_SetLineNumber(py_frame, py_line);
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-#if PY_MAJOR_VERSION < 3
-static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) {
- if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags);
- PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name);
- return -1;
-}
-static void __Pyx_ReleaseBuffer(Py_buffer *view) {
- PyObject *obj = view->obj;
- if (!obj) return;
- if (PyObject_CheckBuffer(obj)) {
- PyBuffer_Release(view);
- return;
- }
- if ((0)) {}
- view->obj = NULL;
- Py_DECREF(obj);
-}
-#endif
-
-
- /* CIntFromPyVerify */
- #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\
- __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0)
-#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\
- __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1)
-#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\
- {\
- func_type value = func_value;\
- if (sizeof(target_type) < sizeof(func_type)) {\
- if (unlikely(value != (func_type) (target_type) value)) {\
- func_type zero = 0;\
- if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\
- return (target_type) -1;\
- if (is_unsigned && unlikely(value < zero))\
- goto raise_neg_overflow;\
- else\
- goto raise_overflow;\
- }\
- }\
- return (target_type) value;\
- }
-
-/* Declarations */
- #if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
- return ::std::complex< float >(x, y);
- }
- #else
- static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
- return x + y*(__pyx_t_float_complex)_Complex_I;
- }
- #endif
-#else
- static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
- __pyx_t_float_complex z;
- z.real = x;
- z.imag = y;
- return z;
- }
-#endif
-
-/* Arithmetic */
- #if CYTHON_CCOMPLEX
-#else
- static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- return (a.real == b.real) && (a.imag == b.imag);
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- z.real = a.real + b.real;
- z.imag = a.imag + b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- z.real = a.real - b.real;
- z.imag = a.imag - b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- z.real = a.real * b.real - a.imag * b.imag;
- z.imag = a.real * b.imag + a.imag * b.real;
- return z;
- }
- #if 1
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- if (b.imag == 0) {
- return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real);
- } else if (fabsf(b.real) >= fabsf(b.imag)) {
- if (b.real == 0 && b.imag == 0) {
- return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.imag);
- } else {
- float r = b.imag / b.real;
- float s = (float)(1.0) / (b.real + b.imag * r);
- return __pyx_t_float_complex_from_parts(
- (a.real + a.imag * r) * s, (a.imag - a.real * r) * s);
- }
- } else {
- float r = b.real / b.imag;
- float s = (float)(1.0) / (b.imag + b.real * r);
- return __pyx_t_float_complex_from_parts(
- (a.real * r + a.imag) * s, (a.imag * r - a.real) * s);
- }
- }
- #else
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- if (b.imag == 0) {
- return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real);
- } else {
- float denom = b.real * b.real + b.imag * b.imag;
- return __pyx_t_float_complex_from_parts(
- (a.real * b.real + a.imag * b.imag) / denom,
- (a.imag * b.real - a.real * b.imag) / denom);
- }
- }
- #endif
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex a) {
- __pyx_t_float_complex z;
- z.real = -a.real;
- z.imag = -a.imag;
- return z;
- }
- static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex a) {
- return (a.real == 0) && (a.imag == 0);
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex a) {
- __pyx_t_float_complex z;
- z.real = a.real;
- z.imag = -a.imag;
- return z;
- }
- #if 1
- static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex z) {
- #if !defined(HAVE_HYPOT) || defined(_MSC_VER)
- return sqrtf(z.real*z.real + z.imag*z.imag);
- #else
- return hypotf(z.real, z.imag);
- #endif
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- float r, lnr, theta, z_r, z_theta;
- if (b.imag == 0 && b.real == (int)b.real) {
- if (b.real < 0) {
- float denom = a.real * a.real + a.imag * a.imag;
- a.real = a.real / denom;
- a.imag = -a.imag / denom;
- b.real = -b.real;
- }
- switch ((int)b.real) {
- case 0:
- z.real = 1;
- z.imag = 0;
- return z;
- case 1:
- return a;
- case 2:
- return __Pyx_c_prod_float(a, a);
- case 3:
- z = __Pyx_c_prod_float(a, a);
- return __Pyx_c_prod_float(z, a);
- case 4:
- z = __Pyx_c_prod_float(a, a);
- return __Pyx_c_prod_float(z, z);
- }
- }
- if (a.imag == 0) {
- if (a.real == 0) {
- return a;
- } else if (b.imag == 0) {
- z.real = powf(a.real, b.real);
- z.imag = 0;
- return z;
- } else if (a.real > 0) {
- r = a.real;
- theta = 0;
- } else {
- r = -a.real;
- theta = atan2f(0.0, -1.0);
- }
- } else {
- r = __Pyx_c_abs_float(a);
- theta = atan2f(a.imag, a.real);
- }
- lnr = logf(r);
- z_r = expf(lnr * b.real - theta * b.imag);
- z_theta = theta * b.real + lnr * b.imag;
- z.real = z_r * cosf(z_theta);
- z.imag = z_r * sinf(z_theta);
- return z;
- }
- #endif
-#endif
-
-/* Declarations */
- #if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
- return ::std::complex< double >(x, y);
- }
- #else
- static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
- return x + y*(__pyx_t_double_complex)_Complex_I;
- }
- #endif
-#else
- static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
- __pyx_t_double_complex z;
- z.real = x;
- z.imag = y;
- return z;
- }
-#endif
-
-/* Arithmetic */
- #if CYTHON_CCOMPLEX
-#else
- static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- return (a.real == b.real) && (a.imag == b.imag);
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- z.real = a.real + b.real;
- z.imag = a.imag + b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- z.real = a.real - b.real;
- z.imag = a.imag - b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- z.real = a.real * b.real - a.imag * b.imag;
- z.imag = a.real * b.imag + a.imag * b.real;
- return z;
- }
- #if 1
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- if (b.imag == 0) {
- return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real);
- } else if (fabs(b.real) >= fabs(b.imag)) {
- if (b.real == 0 && b.imag == 0) {
- return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.imag);
- } else {
- double r = b.imag / b.real;
- double s = (double)(1.0) / (b.real + b.imag * r);
- return __pyx_t_double_complex_from_parts(
- (a.real + a.imag * r) * s, (a.imag - a.real * r) * s);
- }
- } else {
- double r = b.real / b.imag;
- double s = (double)(1.0) / (b.imag + b.real * r);
- return __pyx_t_double_complex_from_parts(
- (a.real * r + a.imag) * s, (a.imag * r - a.real) * s);
- }
- }
- #else
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- if (b.imag == 0) {
- return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real);
- } else {
- double denom = b.real * b.real + b.imag * b.imag;
- return __pyx_t_double_complex_from_parts(
- (a.real * b.real + a.imag * b.imag) / denom,
- (a.imag * b.real - a.real * b.imag) / denom);
- }
- }
- #endif
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex a) {
- __pyx_t_double_complex z;
- z.real = -a.real;
- z.imag = -a.imag;
- return z;
- }
- static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex a) {
- return (a.real == 0) && (a.imag == 0);
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex a) {
- __pyx_t_double_complex z;
- z.real = a.real;
- z.imag = -a.imag;
- return z;
- }
- #if 1
- static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex z) {
- #if !defined(HAVE_HYPOT) || defined(_MSC_VER)
- return sqrt(z.real*z.real + z.imag*z.imag);
- #else
- return hypot(z.real, z.imag);
- #endif
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- double r, lnr, theta, z_r, z_theta;
- if (b.imag == 0 && b.real == (int)b.real) {
- if (b.real < 0) {
- double denom = a.real * a.real + a.imag * a.imag;
- a.real = a.real / denom;
- a.imag = -a.imag / denom;
- b.real = -b.real;
- }
- switch ((int)b.real) {
- case 0:
- z.real = 1;
- z.imag = 0;
- return z;
- case 1:
- return a;
- case 2:
- return __Pyx_c_prod_double(a, a);
- case 3:
- z = __Pyx_c_prod_double(a, a);
- return __Pyx_c_prod_double(z, a);
- case 4:
- z = __Pyx_c_prod_double(a, a);
- return __Pyx_c_prod_double(z, z);
- }
- }
- if (a.imag == 0) {
- if (a.real == 0) {
- return a;
- } else if (b.imag == 0) {
- z.real = pow(a.real, b.real);
- z.imag = 0;
- return z;
- } else if (a.real > 0) {
- r = a.real;
- theta = 0;
- } else {
- r = -a.real;
- theta = atan2(0.0, -1.0);
- }
- } else {
- r = __Pyx_c_abs_double(a);
- theta = atan2(a.imag, a.real);
- }
- lnr = log(r);
- z_r = exp(lnr * b.real - theta * b.imag);
- z_theta = theta * b.real + lnr * b.imag;
- z.real = z_r * cos(z_theta);
- z.imag = z_r * sin(z_theta);
- return z;
- }
- #endif
-#endif
-
-/* CIntToPy */
- static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
-#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
-#pragma GCC diagnostic push
-#pragma GCC diagnostic ignored "-Wconversion"
-#endif
- const int neg_one = (int) -1, const_zero = (int) 0;
-#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
-#pragma GCC diagnostic pop
-#endif
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(int) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(int) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
-#ifdef HAVE_LONG_LONG
- } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) {
- return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
-#endif
- }
- } else {
- if (sizeof(int) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
-#ifdef HAVE_LONG_LONG
- } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) {
- return PyLong_FromLongLong((PY_LONG_LONG) value);
-#endif
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(int),
- little, !is_unsigned);
- }
-}
-
-/* CIntFromPy */
- static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
-#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
-#pragma GCC diagnostic push
-#pragma GCC diagnostic ignored "-Wconversion"
-#endif
- const int neg_one = (int) -1, const_zero = (int) 0;
-#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
-#pragma GCC diagnostic pop
-#endif
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(int) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x))
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- goto raise_neg_overflow;
- }
- return (int) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_USE_PYLONG_INTERNALS
- const digit* digits = ((PyLongObject*)x)->ob_digit;
- switch (Py_SIZE(x)) {
- case 0: return (int) 0;
- case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0])
- case 2:
- if (8 * sizeof(int) > 1 * PyLong_SHIFT) {
- if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
- } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) {
- return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
- }
- }
- break;
- case 3:
- if (8 * sizeof(int) > 2 * PyLong_SHIFT) {
- if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
- } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) {
- return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
- }
- }
- break;
- case 4:
- if (8 * sizeof(int) > 3 * PyLong_SHIFT) {
- if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
- } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) {
- return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
- }
- }
- break;
- }
-#endif
-#if CYTHON_COMPILING_IN_CPYTHON
- if (unlikely(Py_SIZE(x) < 0)) {
- goto raise_neg_overflow;
- }
-#else
- {
- int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
- if (unlikely(result < 0))
- return (int) -1;
- if (unlikely(result == 1))
- goto raise_neg_overflow;
- }
-#endif
- if (sizeof(int) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x))
-#ifdef HAVE_LONG_LONG
- } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) {
- __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
-#endif
- }
- } else {
-#if CYTHON_USE_PYLONG_INTERNALS
- const digit* digits = ((PyLongObject*)x)->ob_digit;
- switch (Py_SIZE(x)) {
- case 0: return (int) 0;
- case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0]))
- case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0])
- case -2:
- if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) {
- if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
- __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
- } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) {
- return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
- }
- }
- break;
- case 2:
- if (8 * sizeof(int) > 1 * PyLong_SHIFT) {
- if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
- } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) {
- return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
- }
- }
- break;
- case -3:
- if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) {
- if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
- __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
- } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) {
- return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
- }
- }
- break;
- case 3:
- if (8 * sizeof(int) > 2 * PyLong_SHIFT) {
- if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
- } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) {
- return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
- }
- }
- break;
- case -4:
- if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) {
- if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
- __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
- } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) {
- return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
- }
- }
- break;
- case 4:
- if (8 * sizeof(int) > 3 * PyLong_SHIFT) {
- if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
- } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) {
- return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
- }
- }
- break;
- }
-#endif
- if (sizeof(int) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x))
-#ifdef HAVE_LONG_LONG
- } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) {
- __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x))
-#endif
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- int val;
- PyObject *v = __Pyx_PyNumber_IntOrLong(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (int) -1;
- }
- } else {
- int val;
- PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
- if (!tmp) return (int) -1;
- val = __Pyx_PyInt_As_int(tmp);
- Py_DECREF(tmp);
- return val;
- }
-raise_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to int");
- return (int) -1;
-raise_neg_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to int");
- return (int) -1;
-}
-
-/* CIntToPy */
- static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
-#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
-#pragma GCC diagnostic push
-#pragma GCC diagnostic ignored "-Wconversion"
-#endif
- const long neg_one = (long) -1, const_zero = (long) 0;
-#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
-#pragma GCC diagnostic pop
-#endif
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(long) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(long) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
-#ifdef HAVE_LONG_LONG
- } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) {
- return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
-#endif
- }
- } else {
- if (sizeof(long) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
-#ifdef HAVE_LONG_LONG
- } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) {
- return PyLong_FromLongLong((PY_LONG_LONG) value);
-#endif
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(long),
- little, !is_unsigned);
- }
-}
-
-/* CIntFromPy */
- static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
-#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
-#pragma GCC diagnostic push
-#pragma GCC diagnostic ignored "-Wconversion"
-#endif
- const long neg_one = (long) -1, const_zero = (long) 0;
-#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
-#pragma GCC diagnostic pop
-#endif
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(long) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x))
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- goto raise_neg_overflow;
- }
- return (long) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_USE_PYLONG_INTERNALS
- const digit* digits = ((PyLongObject*)x)->ob_digit;
- switch (Py_SIZE(x)) {
- case 0: return (long) 0;
- case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0])
- case 2:
- if (8 * sizeof(long) > 1 * PyLong_SHIFT) {
- if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
- } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) {
- return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
- }
- }
- break;
- case 3:
- if (8 * sizeof(long) > 2 * PyLong_SHIFT) {
- if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
- } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) {
- return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
- }
- }
- break;
- case 4:
- if (8 * sizeof(long) > 3 * PyLong_SHIFT) {
- if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
- } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) {
- return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
- }
- }
- break;
- }
-#endif
-#if CYTHON_COMPILING_IN_CPYTHON
- if (unlikely(Py_SIZE(x) < 0)) {
- goto raise_neg_overflow;
- }
-#else
- {
- int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
- if (unlikely(result < 0))
- return (long) -1;
- if (unlikely(result == 1))
- goto raise_neg_overflow;
- }
-#endif
- if (sizeof(long) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x))
-#ifdef HAVE_LONG_LONG
- } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) {
- __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
-#endif
- }
- } else {
-#if CYTHON_USE_PYLONG_INTERNALS
- const digit* digits = ((PyLongObject*)x)->ob_digit;
- switch (Py_SIZE(x)) {
- case 0: return (long) 0;
- case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0]))
- case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0])
- case -2:
- if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) {
- if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
- __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
- } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
- return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
- }
- }
- break;
- case 2:
- if (8 * sizeof(long) > 1 * PyLong_SHIFT) {
- if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
- } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
- return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
- }
- }
- break;
- case -3:
- if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
- if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
- __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
- } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
- return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
- }
- }
- break;
- case 3:
- if (8 * sizeof(long) > 2 * PyLong_SHIFT) {
- if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
- } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
- return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
- }
- }
- break;
- case -4:
- if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
- if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
- __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
- } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
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- }
- break;
- case 4:
- if (8 * sizeof(long) > 3 * PyLong_SHIFT) {
- if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
- } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
- return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
- }
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- break;
- }
-#endif
- if (sizeof(long) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x))
-#ifdef HAVE_LONG_LONG
- } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) {
- __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x))
-#endif
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- long val;
- PyObject *v = __Pyx_PyNumber_IntOrLong(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
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- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (long) -1;
- }
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- long val;
- PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
- if (!tmp) return (long) -1;
- val = __Pyx_PyInt_As_long(tmp);
- Py_DECREF(tmp);
- return val;
- }
-raise_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to long");
- return (long) -1;
-raise_neg_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long) -1;
-}
-
-/* FastTypeChecks */
- #if CYTHON_COMPILING_IN_CPYTHON
-static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) {
- while (a) {
- a = a->tp_base;
- if (a == b)
- return 1;
- }
- return b == &PyBaseObject_Type;
-}
-static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) {
- PyObject *mro;
- if (a == b) return 1;
- mro = a->tp_mro;
- if (likely(mro)) {
- Py_ssize_t i, n;
- n = PyTuple_GET_SIZE(mro);
- for (i = 0; i < n; i++) {
- if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b)
- return 1;
- }
- return 0;
- }
- return __Pyx_InBases(a, b);
-}
-#if PY_MAJOR_VERSION == 2
-static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) {
- PyObject *exception, *value, *tb;
- int res;
- __Pyx_PyThreadState_declare
- __Pyx_PyThreadState_assign
- __Pyx_ErrFetch(&exception, &value, &tb);
- res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0;
- if (unlikely(res == -1)) {
- PyErr_WriteUnraisable(err);
- res = 0;
- }
- if (!res) {
- res = PyObject_IsSubclass(err, exc_type2);
- if (unlikely(res == -1)) {
- PyErr_WriteUnraisable(err);
- res = 0;
- }
- }
- __Pyx_ErrRestore(exception, value, tb);
- return res;
-}
-#else
-static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) {
- int res = exc_type1 ? __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type1) : 0;
- if (!res) {
- res = __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2);
- }
- return res;
-}
-#endif
-static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) {
- Py_ssize_t i, n;
- assert(PyExceptionClass_Check(exc_type));
- n = PyTuple_GET_SIZE(tuple);
-#if PY_MAJOR_VERSION >= 3
- for (i=0; i<n; i++) {
- if (exc_type == PyTuple_GET_ITEM(tuple, i)) return 1;
- }
-#endif
- for (i=0; i<n; i++) {
- PyObject *t = PyTuple_GET_ITEM(tuple, i);
- #if PY_MAJOR_VERSION < 3
- if (likely(exc_type == t)) return 1;
- #endif
- if (likely(PyExceptionClass_Check(t))) {
- if (__Pyx_inner_PyErr_GivenExceptionMatches2(exc_type, NULL, t)) return 1;
- } else {
- }
- }
- return 0;
-}
-static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject* exc_type) {
- if (likely(err == exc_type)) return 1;
- if (likely(PyExceptionClass_Check(err))) {
- if (likely(PyExceptionClass_Check(exc_type))) {
- return __Pyx_inner_PyErr_GivenExceptionMatches2(err, NULL, exc_type);
- } else if (likely(PyTuple_Check(exc_type))) {
- return __Pyx_PyErr_GivenExceptionMatchesTuple(err, exc_type);
- } else {
- }
- }
- return PyErr_GivenExceptionMatches(err, exc_type);
-}
-static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *exc_type1, PyObject *exc_type2) {
- assert(PyExceptionClass_Check(exc_type1));
- assert(PyExceptionClass_Check(exc_type2));
- if (likely(err == exc_type1 || err == exc_type2)) return 1;
- if (likely(PyExceptionClass_Check(err))) {
- return __Pyx_inner_PyErr_GivenExceptionMatches2(err, exc_type1, exc_type2);
- }
- return (PyErr_GivenExceptionMatches(err, exc_type1) || PyErr_GivenExceptionMatches(err, exc_type2));
-}
-#endif
-
-/* CheckBinaryVersion */
- static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- return PyErr_WarnEx(NULL, message, 1);
- }
- return 0;
-}
-
-/* InitStrings */
- static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- if (PyObject_Hash(*t->p) == -1)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) {
- return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str));
-}
-static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) {
- Py_ssize_t ignore;
- return __Pyx_PyObject_AsStringAndSize(o, &ignore);
-}
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
-#if !CYTHON_PEP393_ENABLED
-static const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
- char* defenc_c;
- PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
- if (!defenc) return NULL;
- defenc_c = PyBytes_AS_STRING(defenc);
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- {
- char* end = defenc_c + PyBytes_GET_SIZE(defenc);
- char* c;
- for (c = defenc_c; c < end; c++) {
- if ((unsigned char) (*c) >= 128) {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
- }
- }
-#endif
- *length = PyBytes_GET_SIZE(defenc);
- return defenc_c;
-}
-#else
-static CYTHON_INLINE const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
- if (unlikely(__Pyx_PyUnicode_READY(o) == -1)) return NULL;
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- if (likely(PyUnicode_IS_ASCII(o))) {
- *length = PyUnicode_GET_LENGTH(o);
- return PyUnicode_AsUTF8(o);
- } else {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
-#else
- return PyUnicode_AsUTF8AndSize(o, length);
-#endif
-}
-#endif
-#endif
-static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
- if (
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- __Pyx_sys_getdefaultencoding_not_ascii &&
-#endif
- PyUnicode_Check(o)) {
- return __Pyx_PyUnicode_AsStringAndSize(o, length);
- } else
-#endif
-#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE))
- if (PyByteArray_Check(o)) {
- *length = PyByteArray_GET_SIZE(o);
- return PyByteArray_AS_STRING(o);
- } else
-#endif
- {
- char* result;
- int r = PyBytes_AsStringAndSize(o, &result, length);
- if (unlikely(r < 0)) {
- return NULL;
- } else {
- return result;
- }
- }
-}
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject* x) {
- int retval;
- if (unlikely(!x)) return -1;
- retval = __Pyx_PyObject_IsTrue(x);
- Py_DECREF(x);
- return retval;
-}
-static PyObject* __Pyx_PyNumber_IntOrLongWrongResultType(PyObject* result, const char* type_name) {
-#if PY_MAJOR_VERSION >= 3
- if (PyLong_Check(result)) {
- if (PyErr_WarnFormat(PyExc_DeprecationWarning, 1,
- "__int__ returned non-int (type %.200s). "
- "The ability to return an instance of a strict subclass of int "
- "is deprecated, and may be removed in a future version of Python.",
- Py_TYPE(result)->tp_name)) {
- Py_DECREF(result);
- return NULL;
- }
- return result;
- }
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%.4s__ returned non-%.4s (type %.200s)",
- type_name, type_name, Py_TYPE(result)->tp_name);
- Py_DECREF(result);
- return NULL;
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) {
-#if CYTHON_USE_TYPE_SLOTS
- PyNumberMethods *m;
-#endif
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x) || PyLong_Check(x)))
-#else
- if (likely(PyLong_Check(x)))
-#endif
- return __Pyx_NewRef(x);
-#if CYTHON_USE_TYPE_SLOTS
- m = Py_TYPE(x)->tp_as_number;
- #if PY_MAJOR_VERSION < 3
- if (m && m->nb_int) {
- name = "int";
- res = m->nb_int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = m->nb_long(x);
- }
- #else
- if (likely(m && m->nb_int)) {
- name = "int";
- res = m->nb_int(x);
- }
- #endif
-#else
- if (!PyBytes_CheckExact(x) && !PyUnicode_CheckExact(x)) {
- res = PyNumber_Int(x);
- }
-#endif
- if (likely(res)) {
-#if PY_MAJOR_VERSION < 3
- if (unlikely(!PyInt_Check(res) && !PyLong_Check(res))) {
-#else
- if (unlikely(!PyLong_CheckExact(res))) {
-#endif
- return __Pyx_PyNumber_IntOrLongWrongResultType(res, name);
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject *x;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_CheckExact(b))) {
- if (sizeof(Py_ssize_t) >= sizeof(long))
- return PyInt_AS_LONG(b);
- else
- return PyInt_AsSsize_t(b);
- }
-#endif
- if (likely(PyLong_CheckExact(b))) {
- #if CYTHON_USE_PYLONG_INTERNALS
- const digit* digits = ((PyLongObject*)b)->ob_digit;
- const Py_ssize_t size = Py_SIZE(b);
- if (likely(__Pyx_sst_abs(size) <= 1)) {
- ival = likely(size) ? digits[0] : 0;
- if (size == -1) ival = -ival;
- return ival;
- } else {
- switch (size) {
- case 2:
- if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) {
- return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
- }
- break;
- case -2:
- if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) {
- return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
- }
- break;
- case 3:
- if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) {
- return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
- }
- break;
- case -3:
- if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) {
- return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
- }
- break;
- case 4:
- if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) {
- return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
- }
- break;
- case -4:
- if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) {
- return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
- }
- break;
- }
- }
- #endif
- return PyLong_AsSsize_t(b);
- }
- x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b) {
- return b ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False);
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
- return PyInt_FromSize_t(ival);
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/src/screening/gap_rqtest.pyx b/src/screening/gap_rqtest.pyx
deleted file mode 100644
index 1c71ecbca67287ee052416802de8478ae845fa21..0000000000000000000000000000000000000000
--- a/src/screening/gap_rqtest.pyx
+++ /dev/null
@@ -1,155 +0,0 @@
-# -*- coding: utf-8 -*-
-# Based on https://cython.readthedocs.io/en/latest/src/tutorial/numpy.html
-# https://cython.readthedocs.io/en/latest/src/tutorial/memory_allocation.html
-import numpy as np
-
-from src.screening.ascreening import AbstractGapScreening
-
-
-# "cimport" is used to import special compile-time information
-# about the numpy module (this is stored in a file numpy.pxd which is
-# currently part of the Cython distribution).
-cimport numpy as np
-# from libcpp cimport bool as bool_t
-
-cimport cython
-from cpython.mem cimport PyMem_Malloc, PyMem_Realloc, PyMem_Free
-
-ctypedef np.npy_bool bool_t
-
-
-#(AbstractGapScreening)
-
-cdef class GAP_RQtest:
- """ Generalized test
- """
-
- cdef double *vec_cumsum_gammas
- cdef long *vec_rq
-
- @cython.boundscheck(False) # turn off bounds-checking for entire function
- @cython.wraparound(False) # turn off negative index wrapping for entire function
- def __init__(
- self,
- np.ndarray[np.npy_double, ndim=1] vec_gammas,
- np.ndarray[long, ndim=1] vec_rq,
- ):
-
- cdef int n = vec_gammas.shape[0]
- cdef int i
-
- self.vec_cumsum_gammas = <double*> PyMem_Malloc((n+1) * sizeof(double))
- self.vec_cumsum_gammas[0] = 0
-
- self.vec_rq = <long*> PyMem_Malloc(n * sizeof(long))
-
- for i in range(n):
- self.vec_cumsum_gammas[i+1] = self.vec_cumsum_gammas[i] + vec_gammas[i]
- self.vec_rq[i] = vec_rq[i]
-
-
- def __dealloc__(self):
- PyMem_Free(self.vec_cumsum_gammas) # no-op if self.data is NULL
- PyMem_Free(self.vec_rq)
-
- def get_name(self):
- return "p-test cython"
-
-
- @cython.boundscheck(False) # turn off bounds-checking for entire function
- @cython.wraparound(False) # turn off negative index wrapping for entire function
- def apply_test(self,
- np.ndarray[np.npy_double, ndim=1] Atcabs,
- double gap,
- double lbd,
- np.ndarray[np.npy_double, ndim=1] vec_gammas,
- double offset_radius=0.,
- np.ndarray[long, ndim=1] index=None
- ):
- """ Apply the Gap safe sphere screening test
-
- Implementation of the safe screening test
-
- Parameters
- ----------
- Atcabs : np.ndarray
- vector matA.T @ vecc where vec is dual admissible in absolute value
- size [n]
- gap : positive float
- duality gap
- lbd : positive float
- regularization parameters
- vec_gammas : np.ndarray
- slope parameters
- size [n,]
- offset_radius : float
- additive term added to the redius
- default is 0
- index : np.ndarray
- Array of indices that sort Atu in absolute value
- default is None
-
- Returns
- -------
- calI_screen : np.ndarray
- vector of boolean
- True if screening test passes and False otherwise
- size [n,]
- """
-
- cdef double radius = np.sqrt(2 * gap) + offset_radius
-
- cdef int n = Atcabs.shape[0]
- cdef int k, l, q, r_q
- cdef double lhs
-
- # right-hand side
- cdef np.ndarray[np.npy_double, ndim=1] vec_kappaqr
- vec_kappaqr = np.zeros(n+1, dtype=np.double)
-
- for q in range(1, n+1):
- r_q = self.vec_rq[q-1]
-
- vec_kappaqr[q] += lbd * (self.vec_cumsum_gammas[q] - self.vec_cumsum_gammas[r_q-1])
- vec_kappaqr[q] -= (q - r_q + 1) * radius
-
- # output
- cdef np.ndarray[np.npy_bool, ndim=1] calI_screen = np.ones(n, dtype=bool)
-
- # 1. Sort in descending order
- if index is None:
- index = np.argsort(Atcabs)[::-1]
-
- cdef np.ndarray[np.npy_double, ndim=1] vec_cumsumAtcabs = np.zeros(n+1, dtype=np.double)
- vec_cumsumAtcabs[1:] = np.cumsum(Atcabs[index])
-
- for l in range(n):
- index_l = index[l]
-
- for q in range(1, n+1): # Index are shifted by 1
- r_q = self.vec_rq[q-1]
- # lhs = 0
-
- if r_q >= q:
- lhs = Atcabs[index_l]
-
- # elif index_l < index[r_q-1] or index_l >= index[q-1]:
- elif l < r_q or l > q-1:
- #In this calse |A_{\l}c|_[k] =|Atc|_[k] for the range of k
- lhs = Atcabs[index_l] + vec_cumsumAtcabs[q-1] - vec_cumsumAtcabs[r_q-2]
-
- # for k in range(r_q-1, q-1):
- # lhs += Atcabs[index[k]]
-
- else:
- # print("ici else")
- lhs = vec_cumsumAtcabs[q] - vec_cumsumAtcabs[r_q-2]
- # for k in range(r_q-1, q):
- # lhs += Atcabs[index[k]]
-
- if lhs >= vec_kappaqr[q]:
-
- calI_screen[index_l] = False
- break
-
- return calI_screen
\ No newline at end of file
diff --git a/src/screening/gap_ptest.c b/src/screening/gap_test_all.c
similarity index 88%
rename from src/screening/gap_ptest.c
rename to src/screening/gap_test_all.c
index 1c63f09c0d612340e058ad047767fafa2d20c4df..00a93b305924ba2297d346f92340f40b95d1d162 100644
--- a/src/screening/gap_ptest.c
+++ b/src/screening/gap_test_all.c
@@ -4,12 +4,12 @@
{
"distutils": {
"depends": [],
- "name": "src.screening.gap_ptest",
+ "name": "src.screening.gap_test_all",
"sources": [
- "src/screening/gap_ptest.pyx"
+ "src/screening/gap_test_all.pyx"
]
},
- "module_name": "src.screening.gap_ptest"
+ "module_name": "src.screening.gap_test_all"
}
END: Cython Metadata */
@@ -625,8 +625,8 @@ static CYTHON_INLINE float __PYX_NAN() {
#endif
#endif
-#define __PYX_HAVE__src__screening__gap_ptest
-#define __PYX_HAVE_API__src__screening__gap_ptest
+#define __PYX_HAVE__src__screening__gap_test_all
+#define __PYX_HAVE_API__src__screening__gap_test_all
/* Early includes */
#include <string.h>
#include <stdio.h>
@@ -868,7 +868,7 @@ static const char *__pyx_filename;
static const char *__pyx_f[] = {
- "src/screening/gap_ptest.pyx",
+ "src/screening/gap_test_all.pyx",
"stringsource",
"venv/lib/python3.8/site-packages/numpy/__init__.pxd",
"venv/lib/python3.8/site-packages/Cython/Includes/cpython/type.pxd",
@@ -1099,14 +1099,14 @@ typedef npy_double __pyx_t_5numpy_double_t;
*/
typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
-/* "src/screening/gap_ptest.pyx":18
+/* "src/screening/gap_test_all.pyx":18
* from cpython.mem cimport PyMem_Malloc, PyMem_Realloc, PyMem_Free
*
* ctypedef np.npy_bool bool_t # <<<<<<<<<<<<<<
*
*
*/
-typedef npy_bool __pyx_t_3src_9screening_9gap_ptest_bool_t;
+typedef npy_bool __pyx_t_3src_9screening_12gap_test_all_bool_t;
/* Declarations.proto */
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
@@ -1133,7 +1133,7 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do
/*--- Type declarations ---*/
-struct __pyx_obj_3src_9screening_9gap_ptest_GAP_Ptest;
+struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll;
/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":729
* ctypedef npy_longdouble longdouble_t
@@ -1171,14 +1171,14 @@ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
*/
typedef npy_cdouble __pyx_t_5numpy_complex_t;
-/* "src/screening/gap_ptest.pyx":23
- * #(AbstractGapScreening)
+/* "src/screening/gap_test_all.pyx":21
*
- * cdef class GAP_Ptest: # <<<<<<<<<<<<<<
+ *
+ * cdef class GapTestAll: # <<<<<<<<<<<<<<
* """ Generalized test
* """
*/
-struct __pyx_obj_3src_9screening_9gap_ptest_GAP_Ptest {
+struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll {
PyObject_HEAD
double *vec_cumsum_gammas;
};
@@ -1298,6 +1298,15 @@ static Py_ssize_t __Pyx_minusones[] = { -1, -1, -1, -1, -1, -1, -1, -1 };
static Py_ssize_t __Pyx_zeros[] = { 0, 0, 0, 0, 0, 0, 0, 0 };
#define __Pyx_BufPtrStrided1d(type, buf, i0, s0) (type)((char*)buf + i0 * s0)
+/* PyObjectSetAttrStr.proto */
+#if CYTHON_USE_TYPE_SLOTS
+#define __Pyx_PyObject_DelAttrStr(o,n) __Pyx_PyObject_SetAttrStr(o, n, NULL)
+static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value);
+#else
+#define __Pyx_PyObject_DelAttrStr(o,n) PyObject_DelAttr(o,n)
+#define __Pyx_PyObject_SetAttrStr(o,n,v) PyObject_SetAttr(o,n,v)
+#endif
+
/* PyThreadStateGet.proto */
#if CYTHON_FAST_THREAD_STATE
#define __Pyx_PyThreadState_declare PyThreadState *__pyx_tstate;
@@ -1774,17 +1783,17 @@ static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0;
/* Module declarations from 'cython' */
-/* Module declarations from 'src.screening.gap_ptest' */
-static PyTypeObject *__pyx_ptype_3src_9screening_9gap_ptest_GAP_Ptest = 0;
+/* Module declarations from 'src.screening.gap_test_all' */
+static PyTypeObject *__pyx_ptype_3src_9screening_12gap_test_all_GapTestAll = 0;
static __Pyx_TypeInfo __Pyx_TypeInfo_nn_npy_double = { "npy_double", NULL, sizeof(npy_double), { 0 }, 0, 'R', 0, 0 };
static __Pyx_TypeInfo __Pyx_TypeInfo_long = { "long", NULL, sizeof(long), { 0 }, 0, IS_UNSIGNED(long) ? 'U' : 'I', IS_UNSIGNED(long), 0 };
static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_int_t = { "int_t", NULL, sizeof(__pyx_t_5numpy_int_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_5numpy_int_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_5numpy_int_t), 0 };
static __Pyx_TypeInfo __Pyx_TypeInfo_nn_npy_bool = { "npy_bool", NULL, sizeof(npy_bool), { 0 }, 0, IS_UNSIGNED(npy_bool) ? 'U' : 'I', IS_UNSIGNED(npy_bool), 0 };
-#define __Pyx_MODULE_NAME "src.screening.gap_ptest"
-extern int __pyx_module_is_main_src__screening__gap_ptest;
-int __pyx_module_is_main_src__screening__gap_ptest = 0;
+#define __Pyx_MODULE_NAME "src.screening.gap_test_all"
+extern int __pyx_module_is_main_src__screening__gap_test_all;
+int __pyx_module_is_main_src__screening__gap_test_all = 0;
-/* Implementation of 'src.screening.gap_ptest' */
+/* Implementation of 'src.screening.gap_test_all' */
static PyObject *__pyx_builtin_range;
static PyObject *__pyx_builtin_TypeError;
static PyObject *__pyx_builtin_ImportError;
@@ -1792,7 +1801,7 @@ static const char __pyx_k_np[] = "np";
static const char __pyx_k_gap[] = "gap";
static const char __pyx_k_lbd[] = "lbd";
static const char __pyx_k_main[] = "__main__";
-static const char __pyx_k_name[] = "__name__";
+static const char __pyx_k_name[] = "name";
static const char __pyx_k_sqrt[] = "sqrt";
static const char __pyx_k_test[] = "__test__";
static const char __pyx_k_dtype[] = "dtype";
@@ -1804,20 +1813,22 @@ static const char __pyx_k_Atcabs[] = "Atcabs";
static const char __pyx_k_arange[] = "arange";
static const char __pyx_k_cumsum[] = "cumsum";
static const char __pyx_k_import[] = "__import__";
+static const char __pyx_k_name_2[] = "__name__";
static const char __pyx_k_reduce[] = "__reduce__";
static const char __pyx_k_argsort[] = "argsort";
static const char __pyx_k_getstate[] = "__getstate__";
static const char __pyx_k_setstate[] = "__setstate__";
-static const char __pyx_k_GAP_Ptest[] = "GAP_Ptest";
static const char __pyx_k_TypeError[] = "TypeError";
static const char __pyx_k_reduce_ex[] = "__reduce_ex__";
+static const char __pyx_k_GapTestAll[] = "GapTestAll";
static const char __pyx_k_vec_gammas[] = "vec_gammas";
static const char __pyx_k_ImportError[] = "ImportError";
static const char __pyx_k_offset_radius[] = "offset_radius";
-static const char __pyx_k_p_test_cython[] = "p-test cython";
static const char __pyx_k_reduce_cython[] = "__reduce_cython__";
static const char __pyx_k_setstate_cython[] = "__setstate_cython__";
static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback";
+static const char __pyx_k_coeff_dual_scaling[] = "coeff_dual_scaling";
+static const char __pyx_k_GAP_test_all_cython[] = "GAP test-all (cython)";
static const char __pyx_k_AbstractGapScreening[] = "AbstractGapScreening";
static const char __pyx_k_src_screening_ascreening[] = "src.screening.ascreening";
static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import";
@@ -1825,12 +1836,14 @@ static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath
static const char __pyx_k_self_vec_cumsum_gammas_cannot_be[] = "self.vec_cumsum_gammas cannot be converted to a Python object for pickling";
static PyObject *__pyx_n_s_AbstractGapScreening;
static PyObject *__pyx_n_s_Atcabs;
-static PyObject *__pyx_n_s_GAP_Ptest;
+static PyObject *__pyx_kp_s_GAP_test_all_cython;
+static PyObject *__pyx_n_s_GapTestAll;
static PyObject *__pyx_n_s_ImportError;
static PyObject *__pyx_n_s_TypeError;
static PyObject *__pyx_n_s_arange;
static PyObject *__pyx_n_s_argsort;
static PyObject *__pyx_n_s_cline_in_traceback;
+static PyObject *__pyx_n_s_coeff_dual_scaling;
static PyObject *__pyx_n_s_cumsum;
static PyObject *__pyx_n_s_dtype;
static PyObject *__pyx_n_s_gap;
@@ -1840,12 +1853,12 @@ static PyObject *__pyx_n_s_index;
static PyObject *__pyx_n_s_lbd;
static PyObject *__pyx_n_s_main;
static PyObject *__pyx_n_s_name;
+static PyObject *__pyx_n_s_name_2;
static PyObject *__pyx_n_s_np;
static PyObject *__pyx_n_s_numpy;
static PyObject *__pyx_kp_s_numpy_core_multiarray_failed_to;
static PyObject *__pyx_kp_s_numpy_core_umath_failed_to_impor;
static PyObject *__pyx_n_s_offset_radius;
-static PyObject *__pyx_kp_s_p_test_cython;
static PyObject *__pyx_n_s_range;
static PyObject *__pyx_n_s_reduce;
static PyObject *__pyx_n_s_reduce_cython;
@@ -1858,13 +1871,12 @@ static PyObject *__pyx_n_s_src_screening_ascreening;
static PyObject *__pyx_n_s_test;
static PyObject *__pyx_n_s_vec_gammas;
static PyObject *__pyx_n_s_zeros;
-static int __pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest___init__(struct __pyx_obj_3src_9screening_9gap_ptest_GAP_Ptest *__pyx_v_self, PyArrayObject *__pyx_v_vec_gammas); /* proto */
-static void __pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest_2__dealloc__(struct __pyx_obj_3src_9screening_9gap_ptest_GAP_Ptest *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest_4get_name(CYTHON_UNUSED struct __pyx_obj_3src_9screening_9gap_ptest_GAP_Ptest *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest_6apply_test(CYTHON_UNUSED struct __pyx_obj_3src_9screening_9gap_ptest_GAP_Ptest *__pyx_v_self, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_gap, double __pyx_v_lbd, PyArrayObject *__pyx_v_vec_gammas, double __pyx_v_offset_radius, PyArrayObject *__pyx_v_index); /* proto */
-static PyObject *__pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest_8__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_3src_9screening_9gap_ptest_GAP_Ptest *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest_10__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_3src_9screening_9gap_ptest_GAP_Ptest *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
-static PyObject *__pyx_tp_new_3src_9screening_9gap_ptest_GAP_Ptest(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
+static int __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll___init__(struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *__pyx_v_self, PyArrayObject *__pyx_v_vec_gammas); /* proto */
+static void __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_2__dealloc__(struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_test(CYTHON_UNUSED struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *__pyx_v_self, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_gap, double __pyx_v_lbd, PyArrayObject *__pyx_v_vec_gammas, double __pyx_v_coeff_dual_scaling, double __pyx_v_offset_radius, PyArrayObject *__pyx_v_index); /* proto */
+static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_6__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_8__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
+static PyObject *__pyx_tp_new_3src_9screening_12gap_test_all_GapTestAll(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_int_0;
static PyObject *__pyx_int_1;
static PyObject *__pyx_int_neg_1;
@@ -1875,7 +1887,7 @@ static PyObject *__pyx_tuple__4;
static PyObject *__pyx_tuple__5;
/* Late includes */
-/* "src/screening/gap_ptest.pyx":31
+/* "src/screening/gap_test_all.pyx":29
* @cython.boundscheck(False) # turn off bounds-checking for entire function
* @cython.wraparound(False) # turn off negative index wrapping for entire function
* def __init__( # <<<<<<<<<<<<<<
@@ -1884,8 +1896,8 @@ static PyObject *__pyx_tuple__5;
*/
/* Python wrapper */
-static int __pyx_pw_3src_9screening_9gap_ptest_9GAP_Ptest_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_3src_9screening_9gap_ptest_9GAP_Ptest_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static int __pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyArrayObject *__pyx_v_vec_gammas = 0;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
@@ -1912,7 +1924,7 @@ static int __pyx_pw_3src_9screening_9gap_ptest_9GAP_Ptest_1__init__(PyObject *__
else goto __pyx_L5_argtuple_error;
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) __PYX_ERR(0, 31, __pyx_L3_error)
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) __PYX_ERR(0, 29, __pyx_L3_error)
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
goto __pyx_L5_argtuple_error;
@@ -1923,14 +1935,14 @@ static int __pyx_pw_3src_9screening_9gap_ptest_9GAP_Ptest_1__init__(PyObject *__
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 31, __pyx_L3_error)
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 29, __pyx_L3_error)
__pyx_L3_error:;
- __Pyx_AddTraceback("src.screening.gap_ptest.GAP_Ptest.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("src.screening.gap_test_all.GapTestAll.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_vec_gammas), __pyx_ptype_5numpy_ndarray, 1, "vec_gammas", 0))) __PYX_ERR(0, 32, __pyx_L1_error)
- __pyx_r = __pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest___init__(((struct __pyx_obj_3src_9screening_9gap_ptest_GAP_Ptest *)__pyx_v_self), __pyx_v_vec_gammas);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_vec_gammas), __pyx_ptype_5numpy_ndarray, 1, "vec_gammas", 0))) __PYX_ERR(0, 30, __pyx_L1_error)
+ __pyx_r = __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll___init__(((struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *)__pyx_v_self), __pyx_v_vec_gammas);
/* function exit code */
goto __pyx_L0;
@@ -1941,7 +1953,7 @@ static int __pyx_pw_3src_9screening_9gap_ptest_9GAP_Ptest_1__init__(PyObject *__
return __pyx_r;
}
-static int __pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest___init__(struct __pyx_obj_3src_9screening_9gap_ptest_GAP_Ptest *__pyx_v_self, PyArrayObject *__pyx_v_vec_gammas) {
+static int __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll___init__(struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *__pyx_v_self, PyArrayObject *__pyx_v_vec_gammas) {
int __pyx_v_n;
int __pyx_v_i;
__Pyx_LocalBuf_ND __pyx_pybuffernd_vec_gammas;
@@ -1962,11 +1974,11 @@ static int __pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest___init__(struct __pyx_
__pyx_pybuffernd_vec_gammas.rcbuffer = &__pyx_pybuffer_vec_gammas;
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_vec_gammas.rcbuffer->pybuffer, (PyObject*)__pyx_v_vec_gammas, &__Pyx_TypeInfo_nn_npy_double, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) __PYX_ERR(0, 31, __pyx_L1_error)
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_vec_gammas.rcbuffer->pybuffer, (PyObject*)__pyx_v_vec_gammas, &__Pyx_TypeInfo_nn_npy_double, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) __PYX_ERR(0, 29, __pyx_L1_error)
}
__pyx_pybuffernd_vec_gammas.diminfo[0].strides = __pyx_pybuffernd_vec_gammas.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_vec_gammas.diminfo[0].shape = __pyx_pybuffernd_vec_gammas.rcbuffer->pybuffer.shape[0];
- /* "src/screening/gap_ptest.pyx":35
+ /* "src/screening/gap_test_all.pyx":33
* ):
*
* cdef int n = vec_gammas.shape[0] # <<<<<<<<<<<<<<
@@ -1975,7 +1987,7 @@ static int __pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest___init__(struct __pyx_
*/
__pyx_v_n = (__pyx_v_vec_gammas->dimensions[0]);
- /* "src/screening/gap_ptest.pyx":38
+ /* "src/screening/gap_test_all.pyx":36
* cdef int i
*
* self.vec_cumsum_gammas = <double*> PyMem_Malloc((n+1) * sizeof(double)) # <<<<<<<<<<<<<<
@@ -1984,7 +1996,7 @@ static int __pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest___init__(struct __pyx_
*/
__pyx_v_self->vec_cumsum_gammas = ((double *)PyMem_Malloc(((__pyx_v_n + 1) * (sizeof(double)))));
- /* "src/screening/gap_ptest.pyx":39
+ /* "src/screening/gap_test_all.pyx":37
*
* self.vec_cumsum_gammas = <double*> PyMem_Malloc((n+1) * sizeof(double))
* self.vec_cumsum_gammas[0] = 0 # <<<<<<<<<<<<<<
@@ -1993,7 +2005,7 @@ static int __pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest___init__(struct __pyx_
*/
(__pyx_v_self->vec_cumsum_gammas[0]) = 0.0;
- /* "src/screening/gap_ptest.pyx":41
+ /* "src/screening/gap_test_all.pyx":39
* self.vec_cumsum_gammas[0] = 0
*
* for i in range(n): # <<<<<<<<<<<<<<
@@ -2005,7 +2017,7 @@ static int __pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest___init__(struct __pyx_
for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
__pyx_v_i = __pyx_t_3;
- /* "src/screening/gap_ptest.pyx":42
+ /* "src/screening/gap_test_all.pyx":40
*
* for i in range(n):
* self.vec_cumsum_gammas[i+1] = self.vec_cumsum_gammas[i] + vec_gammas[i] # <<<<<<<<<<<<<<
@@ -2016,7 +2028,16 @@ static int __pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest___init__(struct __pyx_
(__pyx_v_self->vec_cumsum_gammas[(__pyx_v_i + 1)]) = ((__pyx_v_self->vec_cumsum_gammas[__pyx_v_i]) + (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_gammas.rcbuffer->pybuffer.buf, __pyx_t_4, __pyx_pybuffernd_vec_gammas.diminfo[0].strides)));
}
- /* "src/screening/gap_ptest.pyx":31
+ /* "src/screening/gap_test_all.pyx":48
+ * # self.vec_cumsum_gammas = &buf[0]
+ *
+ * self.name = "GAP test-all (cython)" # <<<<<<<<<<<<<<
+ *
+ *
+ */
+ if (__Pyx_PyObject_SetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_name, __pyx_kp_s_GAP_test_all_cython) < 0) __PYX_ERR(0, 48, __pyx_L1_error)
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* @cython.wraparound(False) # turn off negative index wrapping for entire function
* def __init__( # <<<<<<<<<<<<<<
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__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_vec_gammas.rcbuffer->pybuffer);
__Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);}
- __Pyx_AddTraceback("src.screening.gap_ptest.GAP_Ptest.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("src.screening.gap_test_all.GapTestAll.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
goto __pyx_L2;
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return __pyx_r;
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/* Python wrapper */
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-static void __pyx_pw_3src_9screening_9gap_ptest_9GAP_Ptest_3__dealloc__(PyObject *__pyx_v_self) {
+static void __pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
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+ __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_2__dealloc__(((struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *)__pyx_v_self));
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__Pyx_RefNannyFinishContext();
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+static void __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_2__dealloc__(struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__dealloc__", 0);
- /* "src/screening/gap_ptest.pyx":52
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*/
PyMem_Free(__pyx_v_self->vec_cumsum_gammas);
- /* "src/screening/gap_ptest.pyx":51
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* def __dealloc__(self): # <<<<<<<<<<<<<<
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-
-/* Python wrapper */
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-static PyObject *__pyx_pw_3src_9screening_9gap_ptest_9GAP_Ptest_5get_name(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
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- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_kp_s_p_test_cython);
- __pyx_r = __pyx_kp_s_p_test_cython;
- goto __pyx_L0;
-
- /* "src/screening/gap_ptest.pyx":55
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- /* function exit code */
- __pyx_L0:;
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* # @cython.wraparound(False) # turn off negative index wrapping for entire function
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*/
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-static char __pyx_doc_3src_9screening_9gap_ptest_9GAP_Ptest_6apply_test[] = " Apply the Gap safe sphere screening test\n\n Implementation of the safe screening test\n \n Parameters\n ----------\n Atcabs : np.ndarray\n vector matA.T @ vecc where vec is dual admissible in absolute value\n size [n]\n gap : positive float\n duality gap\n lbd : positive float\n regularization parameters\n vec_gammas : np.ndarray\n slope parameters\n size [n,]\n offset_radius : float\n additive term added to the redius\n default is 0\n index : np.ndarray\n Array of indices that sort Atu in absolute value\n default is None\n \n Returns\n -------\n calI_screen : np.ndarray\n vector of boolean\n True if screening test passes and False otherwise\n size [n,]\n ";
-static PyObject *__pyx_pw_3src_9screening_9gap_ptest_9GAP_Ptest_7apply_test(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_5apply_test(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_3src_9screening_12gap_test_all_10GapTestAll_4apply_test[] = " Apply the Gap safe sphere screening test\n\n Implementation of the safe screening test\n \n Parameters\n ----------\n Atcabs : np.ndarray\n vector matA.T @ vecc where vec is dual admissible in absolute value\n size [n]\n gap : positive float\n duality gap\n lbd : positive float\n regularization parameters\n vec_gammas : np.ndarray\n slope parameters\n size [n,]\n coeff_dual_scaling : positif float\n If coeff_dual_scaling is not feasible, dual scaling factor\n such taht vecu / coeff_dual_scaling os dual feasible\n Here for code optimization purposes\n Default value is 1. (vecu is feasible)\n offset_radius : float\n additive term added to the redius\n default is 0\n index : np.ndarray\n Array of indices that sort Atu in absolute value\n default is None\n \n Returns\n -------\n calI_screen : np.ndarray\n vector of boolean\n True if screening test passes and False otherwise\n size [n,]\n ";
+static PyObject *__pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_5apply_test(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyArrayObject *__pyx_v_Atcabs = 0;
double __pyx_v_gap;
double __pyx_v_lbd;
PyArrayObject *__pyx_v_vec_gammas = 0;
+ double __pyx_v_coeff_dual_scaling;
double __pyx_v_offset_radius;
PyArrayObject *__pyx_v_index = 0;
int __pyx_lineno = 0;
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- PyObject* values[6] = {0,0,0,0,0,0};
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_Atcabs,&__pyx_n_s_gap,&__pyx_n_s_lbd,&__pyx_n_s_vec_gammas,&__pyx_n_s_coeff_dual_scaling,&__pyx_n_s_offset_radius,&__pyx_n_s_index,0};
+ PyObject* values[7] = {0,0,0,0,0,0,0};
- /* "src/screening/gap_ptest.pyx":67
- * np.ndarray[np.npy_double, ndim=1] vec_gammas,
+ /* "src/screening/gap_test_all.pyx":64
+ * double coeff_dual_scaling =1.,
* double offset_radius=0.,
* np.ndarray[long, ndim=1] index=None # <<<<<<<<<<<<<<
* ):
* """ Apply the Gap safe sphere screening test
*/
- values[5] = (PyObject *)((PyArrayObject *)Py_None);
+ values[6] = (PyObject *)((PyArrayObject *)Py_None);
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
switch (pos_args) {
+ case 7: values[6] = PyTuple_GET_ITEM(__pyx_args, 6);
+ CYTHON_FALLTHROUGH;
case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
CYTHON_FALLTHROUGH;
case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
@@ -2205,38 +2176,46 @@ static PyObject *__pyx_pw_3src_9screening_9gap_ptest_9GAP_Ptest_7apply_test(PyOb
case 1:
if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_gap)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("apply_test", 0, 4, 6, 1); __PYX_ERR(0, 61, __pyx_L3_error)
+ __Pyx_RaiseArgtupleInvalid("apply_test", 0, 4, 7, 1); __PYX_ERR(0, 57, __pyx_L3_error)
}
CYTHON_FALLTHROUGH;
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if (likely((values[2] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_lbd)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("apply_test", 0, 4, 6, 2); __PYX_ERR(0, 61, __pyx_L3_error)
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CYTHON_FALLTHROUGH;
case 3:
if (likely((values[3] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_vec_gammas)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("apply_test", 0, 4, 6, 3); __PYX_ERR(0, 61, __pyx_L3_error)
+ __Pyx_RaiseArgtupleInvalid("apply_test", 0, 4, 7, 3); __PYX_ERR(0, 57, __pyx_L3_error)
}
CYTHON_FALLTHROUGH;
case 4:
if (kw_args > 0) {
- PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_offset_radius);
+ PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_coeff_dual_scaling);
if (value) { values[4] = value; kw_args--; }
}
CYTHON_FALLTHROUGH;
case 5:
if (kw_args > 0) {
- PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_index);
+ PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_offset_radius);
if (value) { values[5] = value; kw_args--; }
}
+ CYTHON_FALLTHROUGH;
+ case 6:
+ if (kw_args > 0) {
+ PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_index);
+ if (value) { values[6] = value; kw_args--; }
+ }
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "apply_test") < 0)) __PYX_ERR(0, 61, __pyx_L3_error)
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "apply_test") < 0)) __PYX_ERR(0, 57, __pyx_L3_error)
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
+ case 7: values[6] = PyTuple_GET_ITEM(__pyx_args, 6);
+ CYTHON_FALLTHROUGH;
case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
CYTHON_FALLTHROUGH;
case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
@@ -2250,30 +2229,35 @@ static PyObject *__pyx_pw_3src_9screening_9gap_ptest_9GAP_Ptest_7apply_test(PyOb
}
}
__pyx_v_Atcabs = ((PyArrayObject *)values[0]);
- __pyx_v_gap = __pyx_PyFloat_AsDouble(values[1]); if (unlikely((__pyx_v_gap == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 63, __pyx_L3_error)
- __pyx_v_lbd = __pyx_PyFloat_AsDouble(values[2]); if (unlikely((__pyx_v_lbd == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 64, __pyx_L3_error)
+ __pyx_v_gap = __pyx_PyFloat_AsDouble(values[1]); if (unlikely((__pyx_v_gap == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 59, __pyx_L3_error)
+ __pyx_v_lbd = __pyx_PyFloat_AsDouble(values[2]); if (unlikely((__pyx_v_lbd == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 60, __pyx_L3_error)
__pyx_v_vec_gammas = ((PyArrayObject *)values[3]);
if (values[4]) {
- __pyx_v_offset_radius = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_offset_radius == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 66, __pyx_L3_error)
+ __pyx_v_coeff_dual_scaling = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_coeff_dual_scaling == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 62, __pyx_L3_error)
+ } else {
+ __pyx_v_coeff_dual_scaling = ((double)1.);
+ }
+ if (values[5]) {
+ __pyx_v_offset_radius = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_offset_radius == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 63, __pyx_L3_error)
} else {
__pyx_v_offset_radius = ((double)0.);
}
- __pyx_v_index = ((PyArrayObject *)values[5]);
+ __pyx_v_index = ((PyArrayObject *)values[6]);
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("apply_test", 0, 4, 6, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 61, __pyx_L3_error)
+ __Pyx_RaiseArgtupleInvalid("apply_test", 0, 4, 7, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 57, __pyx_L3_error)
__pyx_L3_error:;
- __Pyx_AddTraceback("src.screening.gap_ptest.GAP_Ptest.apply_test", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("src.screening.gap_test_all.GapTestAll.apply_test", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_Atcabs), __pyx_ptype_5numpy_ndarray, 1, "Atcabs", 0))) __PYX_ERR(0, 62, __pyx_L1_error)
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_vec_gammas), __pyx_ptype_5numpy_ndarray, 1, "vec_gammas", 0))) __PYX_ERR(0, 65, __pyx_L1_error)
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_index), __pyx_ptype_5numpy_ndarray, 1, "index", 0))) __PYX_ERR(0, 67, __pyx_L1_error)
- __pyx_r = __pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest_6apply_test(((struct __pyx_obj_3src_9screening_9gap_ptest_GAP_Ptest *)__pyx_v_self), __pyx_v_Atcabs, __pyx_v_gap, __pyx_v_lbd, __pyx_v_vec_gammas, __pyx_v_offset_radius, __pyx_v_index);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_Atcabs), __pyx_ptype_5numpy_ndarray, 1, "Atcabs", 0))) __PYX_ERR(0, 58, __pyx_L1_error)
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_vec_gammas), __pyx_ptype_5numpy_ndarray, 1, "vec_gammas", 0))) __PYX_ERR(0, 61, __pyx_L1_error)
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_index), __pyx_ptype_5numpy_ndarray, 1, "index", 0))) __PYX_ERR(0, 64, __pyx_L1_error)
+ __pyx_r = __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_test(((struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *)__pyx_v_self), __pyx_v_Atcabs, __pyx_v_gap, __pyx_v_lbd, __pyx_v_vec_gammas, __pyx_v_coeff_dual_scaling, __pyx_v_offset_radius, __pyx_v_index);
- /* "src/screening/gap_ptest.pyx":61
+ /* "src/screening/gap_test_all.pyx":57
* @cython.boundscheck(False) # turn off bounds-checking for entire function
* # @cython.wraparound(False) # turn off negative index wrapping for entire function
* def apply_test(self, # <<<<<<<<<<<<<<
@@ -2290,8 +2274,9 @@ static PyObject *__pyx_pw_3src_9screening_9gap_ptest_9GAP_Ptest_7apply_test(PyOb
return __pyx_r;
}
-static PyObject *__pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest_6apply_test(CYTHON_UNUSED struct __pyx_obj_3src_9screening_9gap_ptest_GAP_Ptest *__pyx_v_self, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_gap, double __pyx_v_lbd, PyArrayObject *__pyx_v_vec_gammas, double __pyx_v_offset_radius, PyArrayObject *__pyx_v_index) {
+static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_test(CYTHON_UNUSED struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *__pyx_v_self, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_gap, double __pyx_v_lbd, PyArrayObject *__pyx_v_vec_gammas, double __pyx_v_coeff_dual_scaling, double __pyx_v_offset_radius, PyArrayObject *__pyx_v_index) {
double __pyx_v_radius;
+ PyArrayObject *__pyx_v_coeff_lbd_gamma = 0;
int __pyx_v_n;
int __pyx_v_k;
int __pyx_v_q;
@@ -2310,6 +2295,8 @@ static PyObject *__pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest_6apply_test(CYTH
__Pyx_Buffer __pyx_pybuffer_Atcabs;
__Pyx_LocalBuf_ND __pyx_pybuffernd_calI_screen;
__Pyx_Buffer __pyx_pybuffer_calI_screen;
+ __Pyx_LocalBuf_ND __pyx_pybuffernd_coeff_lbd_gamma;
+ __Pyx_Buffer __pyx_pybuffer_coeff_lbd_gamma;
__Pyx_LocalBuf_ND __pyx_pybuffernd_index;
__Pyx_Buffer __pyx_pybuffer_index;
__Pyx_LocalBuf_ND __pyx_pybuffernd_vec_f;
@@ -2326,30 +2313,35 @@ static PyObject *__pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest_6apply_test(CYTH
PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
PyObject *__pyx_t_4 = NULL;
- double __pyx_t_5;
- PyArrayObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_5 = NULL;
+ double __pyx_t_6;
PyArrayObject *__pyx_t_7 = NULL;
PyArrayObject *__pyx_t_8 = NULL;
- int __pyx_t_9;
- int __pyx_t_10;
- PyArrayObject *__pyx_t_11 = NULL;
+ PyArrayObject *__pyx_t_9 = NULL;
+ PyArrayObject *__pyx_t_10 = NULL;
+ int __pyx_t_11;
int __pyx_t_12;
- PyObject *__pyx_t_13 = NULL;
- PyObject *__pyx_t_14 = NULL;
+ PyArrayObject *__pyx_t_13 = NULL;
+ int __pyx_t_14;
PyObject *__pyx_t_15 = NULL;
PyObject *__pyx_t_16 = NULL;
- PyArrayObject *__pyx_t_17 = NULL;
- Py_ssize_t __pyx_t_18;
+ PyObject *__pyx_t_17 = NULL;
+ PyArrayObject *__pyx_t_18 = NULL;
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* )[::-1] # <<<<<<<<<<<<<<
*
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*/
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* )[::-1]
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+ * cdef double best_bound_q = vec_f[0] - coeff_lbd_gamma[0] # <<<<<<<<<<<<<<
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*/
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+ if (__pyx_t_19 < 0) __pyx_t_19 += __pyx_pybuffernd_vec_f.diminfo[0].shape;
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+ if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_pybuffernd_coeff_lbd_gamma.diminfo[0].shape;
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- /* "src/screening/gap_ptest.pyx":128
+ /* "src/screening/gap_test_all.pyx":132
*
- * cdef double best_bound_q = vec_f[0] - lbd * vec_gammas[0]
+ * cdef double best_bound_q = vec_f[0] - coeff_lbd_gamma[0]
* cdef double curr_bound_q = 0. # <<<<<<<<<<<<<<
* cdef double best_bound_p = vec_f[0]
* cdef double curr_bound_p = 0.
*/
__pyx_v_curr_bound_q = 0.;
- /* "src/screening/gap_ptest.pyx":129
- * cdef double best_bound_q = vec_f[0] - lbd * vec_gammas[0]
+ /* "src/screening/gap_test_all.pyx":133
+ * cdef double best_bound_q = vec_f[0] - coeff_lbd_gamma[0]
* cdef double curr_bound_q = 0.
* cdef double best_bound_p = vec_f[0] # <<<<<<<<<<<<<<
* cdef double curr_bound_p = 0.
* for k in range(2, n+1):
*/
- __pyx_t_19 = 0;
- if (__pyx_t_19 < 0) __pyx_t_19 += __pyx_pybuffernd_vec_f.diminfo[0].shape;
- __pyx_v_best_bound_p = (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_f.rcbuffer->pybuffer.buf, __pyx_t_19, __pyx_pybuffernd_vec_f.diminfo[0].strides));
+ __pyx_t_20 = 0;
+ if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_pybuffernd_vec_f.diminfo[0].shape;
+ __pyx_v_best_bound_p = (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_f.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_vec_f.diminfo[0].strides));
- /* "src/screening/gap_ptest.pyx":130
+ /* "src/screening/gap_test_all.pyx":134
* cdef double curr_bound_q = 0.
* cdef double best_bound_p = vec_f[0]
* cdef double curr_bound_p = 0. # <<<<<<<<<<<<<<
@@ -2774,40 +2792,40 @@ static PyObject *__pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest_6apply_test(CYTH
*/
__pyx_v_curr_bound_p = 0.;
- /* "src/screening/gap_ptest.pyx":131
+ /* "src/screening/gap_test_all.pyx":135
* cdef double best_bound_p = vec_f[0]
* cdef double curr_bound_p = 0.
* for k in range(2, n+1): # <<<<<<<<<<<<<<
* #+1 is to match paper index
*
*/
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- __pyx_v_k = __pyx_t_12;
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+ __pyx_t_22 = __pyx_t_21;
+ for (__pyx_t_14 = 2; __pyx_t_14 < __pyx_t_22; __pyx_t_14+=1) {
+ __pyx_v_k = __pyx_t_14;
- /* "src/screening/gap_ptest.pyx":135
+ /* "src/screening/gap_test_all.pyx":139
*
* # 1. Evaluate p*
* curr_bound_p = vec_f[k-1] # <<<<<<<<<<<<<<
* if curr_bound_p > best_bound_p:
* best_bound_p = curr_bound_p
*/
- __pyx_t_19 = (__pyx_v_k - 1);
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- __pyx_v_curr_bound_p = (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_f.rcbuffer->pybuffer.buf, __pyx_t_19, __pyx_pybuffernd_vec_f.diminfo[0].strides));
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+ if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_pybuffernd_vec_f.diminfo[0].shape;
+ __pyx_v_curr_bound_p = (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_f.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_vec_f.diminfo[0].strides));
- /* "src/screening/gap_ptest.pyx":136
+ /* "src/screening/gap_test_all.pyx":140
* # 1. Evaluate p*
* curr_bound_p = vec_f[k-1]
* if curr_bound_p > best_bound_p: # <<<<<<<<<<<<<<
* best_bound_p = curr_bound_p
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*/
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- /* "src/screening/gap_ptest.pyx":137
+ /* "src/screening/gap_test_all.pyx":141
* curr_bound_p = vec_f[k-1]
* if curr_bound_p > best_bound_p:
* best_bound_p = curr_bound_p # <<<<<<<<<<<<<<
@@ -2816,18 +2834,18 @@ static PyObject *__pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest_6apply_test(CYTH
*/
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- /* "src/screening/gap_ptest.pyx":138
+ /* "src/screening/gap_test_all.pyx":142
* if curr_bound_p > best_bound_p:
* best_bound_p = curr_bound_p
* vec_p_star[k] = k # <<<<<<<<<<<<<<
* else:
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*/
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+ if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_pybuffernd_vec_p_star.diminfo[0].shape;
+ *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int_t *, __pyx_pybuffernd_vec_p_star.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_vec_p_star.diminfo[0].strides) = __pyx_v_k;
- /* "src/screening/gap_ptest.pyx":136
+ /* "src/screening/gap_test_all.pyx":140
* # 1. Evaluate p*
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@@ -2837,7 +2855,7 @@ static PyObject *__pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest_6apply_test(CYTH
goto __pyx_L6;
}
- /* "src/screening/gap_ptest.pyx":140
+ /* "src/screening/gap_test_all.pyx":144
* vec_p_star[k] = k
* else:
* vec_p_star[k] = vec_p_star[k-1] # <<<<<<<<<<<<<<
@@ -2845,39 +2863,39 @@ static PyObject *__pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest_6apply_test(CYTH
* # 1. Evaluate q*
*/
/*else*/ {
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+ if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_pybuffernd_vec_p_star.diminfo[0].shape;
+ __pyx_t_19 = __pyx_v_k;
if (__pyx_t_19 < 0) __pyx_t_19 += __pyx_pybuffernd_vec_p_star.diminfo[0].shape;
- __pyx_t_18 = __pyx_v_k;
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+ *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int_t *, __pyx_pybuffernd_vec_p_star.rcbuffer->pybuffer.buf, __pyx_t_19, __pyx_pybuffernd_vec_p_star.diminfo[0].strides) = (*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int_t *, __pyx_pybuffernd_vec_p_star.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_vec_p_star.diminfo[0].strides));
}
__pyx_L6:;
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+ /* "src/screening/gap_test_all.pyx":147
*
* # 1. Evaluate q*
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+ * curr_bound_q = vec_f[k-1] - coeff_lbd_gamma[k-1] # <<<<<<<<<<<<<<
* if curr_bound_q > best_bound_q:
* best_bound_q = curr_bound_q
*/
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+ if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_pybuffernd_vec_f.diminfo[0].shape;
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- if (__pyx_t_19 < 0) __pyx_t_19 += __pyx_pybuffernd_vec_f.diminfo[0].shape;
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- __pyx_v_curr_bound_q = ((*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_f.rcbuffer->pybuffer.buf, __pyx_t_19, __pyx_pybuffernd_vec_f.diminfo[0].strides)) - (__pyx_v_lbd * (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_gammas.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_vec_gammas.diminfo[0].strides))));
+ if (__pyx_t_19 < 0) __pyx_t_19 += __pyx_pybuffernd_coeff_lbd_gamma.diminfo[0].shape;
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- /* "src/screening/gap_ptest.pyx":144
+ /* "src/screening/gap_test_all.pyx":148
* # 1. Evaluate q*
- * curr_bound_q = vec_f[k-1] - lbd * vec_gammas[k-1]
+ * curr_bound_q = vec_f[k-1] - coeff_lbd_gamma[k-1]
* if curr_bound_q > best_bound_q: # <<<<<<<<<<<<<<
* best_bound_q = curr_bound_q
* vec_q_star[k] = k
*/
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- if (__pyx_t_10) {
+ __pyx_t_12 = ((__pyx_v_curr_bound_q > __pyx_v_best_bound_q) != 0);
+ if (__pyx_t_12) {
- /* "src/screening/gap_ptest.pyx":145
- * curr_bound_q = vec_f[k-1] - lbd * vec_gammas[k-1]
+ /* "src/screening/gap_test_all.pyx":149
+ * curr_bound_q = vec_f[k-1] - coeff_lbd_gamma[k-1]
* if curr_bound_q > best_bound_q:
* best_bound_q = curr_bound_q # <<<<<<<<<<<<<<
* vec_q_star[k] = k
@@ -2885,20 +2903,20 @@ static PyObject *__pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest_6apply_test(CYTH
*/
__pyx_v_best_bound_q = __pyx_v_curr_bound_q;
- /* "src/screening/gap_ptest.pyx":146
+ /* "src/screening/gap_test_all.pyx":150
* if curr_bound_q > best_bound_q:
* best_bound_q = curr_bound_q
* vec_q_star[k] = k # <<<<<<<<<<<<<<
* else:
* vec_q_star[k] = vec_q_star[k-1]
*/
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- if (__pyx_t_18 < 0) __pyx_t_18 += __pyx_pybuffernd_vec_q_star.diminfo[0].shape;
- *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int_t *, __pyx_pybuffernd_vec_q_star.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_vec_q_star.diminfo[0].strides) = __pyx_v_k;
+ __pyx_t_19 = __pyx_v_k;
+ if (__pyx_t_19 < 0) __pyx_t_19 += __pyx_pybuffernd_vec_q_star.diminfo[0].shape;
+ *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int_t *, __pyx_pybuffernd_vec_q_star.rcbuffer->pybuffer.buf, __pyx_t_19, __pyx_pybuffernd_vec_q_star.diminfo[0].strides) = __pyx_v_k;
- /* "src/screening/gap_ptest.pyx":144
+ /* "src/screening/gap_test_all.pyx":148
* # 1. Evaluate q*
- * curr_bound_q = vec_f[k-1] - lbd * vec_gammas[k-1]
+ * curr_bound_q = vec_f[k-1] - coeff_lbd_gamma[k-1]
* if curr_bound_q > best_bound_q: # <<<<<<<<<<<<<<
* best_bound_q = curr_bound_q
* vec_q_star[k] = k
@@ -2906,7 +2924,7 @@ static PyObject *__pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest_6apply_test(CYTH
goto __pyx_L7;
}
- /* "src/screening/gap_ptest.pyx":148
+ /* "src/screening/gap_test_all.pyx":152
* vec_q_star[k] = k
* else:
* vec_q_star[k] = vec_q_star[k-1] # <<<<<<<<<<<<<<
@@ -2914,95 +2932,95 @@ static PyObject *__pyx_pf_3src_9screening_9gap_ptest_9GAP_Ptest_6apply_test(CYTH
* # 3. Tests
*/
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- if (__pyx_t_18 < 0) __pyx_t_18 += __pyx_pybuffernd_vec_q_star.diminfo[0].shape;
- __pyx_t_19 = __pyx_v_k;
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+static PyObject *__pyx_tp_new_3src_9screening_12gap_test_all_GapTestAll(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
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return o;
}
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- {"__setstate_cython__", (PyCFunction)__pyx_pw_3src_9screening_9gap_ptest_9GAP_Ptest_11__setstate_cython__, METH_O, 0},
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+ {"apply_test", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_5apply_test, METH_VARARGS|METH_KEYWORDS, __pyx_doc_3src_9screening_12gap_test_all_10GapTestAll_4apply_test},
+ {"__reduce_cython__", (PyCFunction)__pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_7__reduce_cython__, METH_NOARGS, 0},
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{0, 0, 0, 0}
};
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PyVarObject_HEAD_INIT(0, 0)
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- sizeof(struct __pyx_obj_3src_9screening_9gap_ptest_GAP_Ptest), /*tp_basicsize*/
+ "src.screening.gap_test_all.GapTestAll", /*tp_name*/
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0, /*tp_itemsize*/
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0, /*tp_alloc*/
- __pyx_tp_new_3src_9screening_9gap_ptest_GAP_Ptest, /*tp_new*/
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static PyObject* __pyx_pymod_create(PyObject *spec, PyModuleDef *def); /*proto*/
-static int __pyx_pymod_exec_gap_ptest(PyObject* module); /*proto*/
+static int __pyx_pymod_exec_gap_test_all(PyObject* module); /*proto*/
static PyModuleDef_Slot __pyx_moduledef_slots[] = {
{Py_mod_create, (void*)__pyx_pymod_create},
- {Py_mod_exec, (void*)__pyx_pymod_exec_gap_ptest},
+ {Py_mod_exec, (void*)__pyx_pymod_exec_gap_test_all},
{0, NULL}
};
#endif
static struct PyModuleDef __pyx_moduledef = {
PyModuleDef_HEAD_INIT,
- "gap_ptest",
+ "gap_test_all",
0, /* m_doc */
#if CYTHON_PEP489_MULTI_PHASE_INIT
0, /* m_size */
@@ -4506,12 +4526,14 @@ static struct PyModuleDef __pyx_moduledef = {
static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_AbstractGapScreening, __pyx_k_AbstractGapScreening, sizeof(__pyx_k_AbstractGapScreening), 0, 0, 1, 1},
{&__pyx_n_s_Atcabs, __pyx_k_Atcabs, sizeof(__pyx_k_Atcabs), 0, 0, 1, 1},
- {&__pyx_n_s_GAP_Ptest, __pyx_k_GAP_Ptest, sizeof(__pyx_k_GAP_Ptest), 0, 0, 1, 1},
+ {&__pyx_kp_s_GAP_test_all_cython, __pyx_k_GAP_test_all_cython, sizeof(__pyx_k_GAP_test_all_cython), 0, 0, 1, 0},
+ {&__pyx_n_s_GapTestAll, __pyx_k_GapTestAll, sizeof(__pyx_k_GapTestAll), 0, 0, 1, 1},
{&__pyx_n_s_ImportError, __pyx_k_ImportError, sizeof(__pyx_k_ImportError), 0, 0, 1, 1},
{&__pyx_n_s_TypeError, __pyx_k_TypeError, sizeof(__pyx_k_TypeError), 0, 0, 1, 1},
{&__pyx_n_s_arange, __pyx_k_arange, sizeof(__pyx_k_arange), 0, 0, 1, 1},
{&__pyx_n_s_argsort, __pyx_k_argsort, sizeof(__pyx_k_argsort), 0, 0, 1, 1},
{&__pyx_n_s_cline_in_traceback, __pyx_k_cline_in_traceback, sizeof(__pyx_k_cline_in_traceback), 0, 0, 1, 1},
+ {&__pyx_n_s_coeff_dual_scaling, __pyx_k_coeff_dual_scaling, sizeof(__pyx_k_coeff_dual_scaling), 0, 0, 1, 1},
{&__pyx_n_s_cumsum, __pyx_k_cumsum, sizeof(__pyx_k_cumsum), 0, 0, 1, 1},
{&__pyx_n_s_dtype, __pyx_k_dtype, sizeof(__pyx_k_dtype), 0, 0, 1, 1},
{&__pyx_n_s_gap, __pyx_k_gap, sizeof(__pyx_k_gap), 0, 0, 1, 1},
@@ -4521,12 +4543,12 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_lbd, __pyx_k_lbd, sizeof(__pyx_k_lbd), 0, 0, 1, 1},
{&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1},
{&__pyx_n_s_name, __pyx_k_name, sizeof(__pyx_k_name), 0, 0, 1, 1},
+ {&__pyx_n_s_name_2, __pyx_k_name_2, sizeof(__pyx_k_name_2), 0, 0, 1, 1},
{&__pyx_n_s_np, __pyx_k_np, sizeof(__pyx_k_np), 0, 0, 1, 1},
{&__pyx_n_s_numpy, __pyx_k_numpy, sizeof(__pyx_k_numpy), 0, 0, 1, 1},
{&__pyx_kp_s_numpy_core_multiarray_failed_to, __pyx_k_numpy_core_multiarray_failed_to, sizeof(__pyx_k_numpy_core_multiarray_failed_to), 0, 0, 1, 0},
{&__pyx_kp_s_numpy_core_umath_failed_to_impor, __pyx_k_numpy_core_umath_failed_to_impor, sizeof(__pyx_k_numpy_core_umath_failed_to_impor), 0, 0, 1, 0},
{&__pyx_n_s_offset_radius, __pyx_k_offset_radius, sizeof(__pyx_k_offset_radius), 0, 0, 1, 1},
- {&__pyx_kp_s_p_test_cython, __pyx_k_p_test_cython, sizeof(__pyx_k_p_test_cython), 0, 0, 1, 0},
{&__pyx_n_s_range, __pyx_k_range, sizeof(__pyx_k_range), 0, 0, 1, 1},
{&__pyx_n_s_reduce, __pyx_k_reduce, sizeof(__pyx_k_reduce), 0, 0, 1, 1},
{&__pyx_n_s_reduce_cython, __pyx_k_reduce_cython, sizeof(__pyx_k_reduce_cython), 0, 0, 1, 1},
@@ -4542,7 +4564,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{0, 0, 0, 0, 0, 0, 0}
};
static CYTHON_SMALL_CODE int __Pyx_InitCachedBuiltins(void) {
- __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) __PYX_ERR(0, 41, __pyx_L1_error)
+ __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) __PYX_ERR(0, 39, __pyx_L1_error)
__pyx_builtin_TypeError = __Pyx_GetBuiltinName(__pyx_n_s_TypeError); if (!__pyx_builtin_TypeError) __PYX_ERR(1, 2, __pyx_L1_error)
__pyx_builtin_ImportError = __Pyx_GetBuiltinName(__pyx_n_s_ImportError); if (!__pyx_builtin_ImportError) __PYX_ERR(2, 945, __pyx_L1_error)
return 0;
@@ -4554,14 +4576,14 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) {
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);
- /* "src/screening/gap_ptest.pyx":120
+ /* "src/screening/gap_test_all.pyx":124
* # 1. Sort in descending order
* if index is None:
* index = np.argsort(Atcabs)[::-1] # <<<<<<<<<<<<<<
*
* # 2. Precomputing quantities
*/
- __pyx_slice_ = PySlice_New(Py_None, Py_None, __pyx_int_neg_1); if (unlikely(!__pyx_slice_)) __PYX_ERR(0, 120, __pyx_L1_error)
+ __pyx_slice_ = PySlice_New(Py_None, Py_None, __pyx_int_neg_1); if (unlikely(!__pyx_slice_)) __PYX_ERR(0, 124, __pyx_L1_error)
__Pyx_GOTREF(__pyx_slice_);
__Pyx_GIVEREF(__pyx_slice_);
@@ -4661,16 +4683,16 @@ static int __Pyx_modinit_type_init_code(void) {
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__Pyx_modinit_type_init_code", 0);
/*--- Type init code ---*/
- if (PyType_Ready(&__pyx_type_3src_9screening_9gap_ptest_GAP_Ptest) < 0) __PYX_ERR(0, 23, __pyx_L1_error)
+ if (PyType_Ready(&__pyx_type_3src_9screening_12gap_test_all_GapTestAll) < 0) __PYX_ERR(0, 21, __pyx_L1_error)
#if PY_VERSION_HEX < 0x030800B1
- __pyx_type_3src_9screening_9gap_ptest_GAP_Ptest.tp_print = 0;
+ __pyx_type_3src_9screening_12gap_test_all_GapTestAll.tp_print = 0;
#endif
- if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_3src_9screening_9gap_ptest_GAP_Ptest.tp_dictoffset && __pyx_type_3src_9screening_9gap_ptest_GAP_Ptest.tp_getattro == PyObject_GenericGetAttr)) {
- __pyx_type_3src_9screening_9gap_ptest_GAP_Ptest.tp_getattro = __Pyx_PyObject_GenericGetAttr;
+ if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_3src_9screening_12gap_test_all_GapTestAll.tp_dictoffset && __pyx_type_3src_9screening_12gap_test_all_GapTestAll.tp_getattro == PyObject_GenericGetAttr)) {
+ __pyx_type_3src_9screening_12gap_test_all_GapTestAll.tp_getattro = __Pyx_PyObject_GenericGetAttr;
}
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s_GAP_Ptest, (PyObject *)&__pyx_type_3src_9screening_9gap_ptest_GAP_Ptest) < 0) __PYX_ERR(0, 23, __pyx_L1_error)
- if (__Pyx_setup_reduce((PyObject*)&__pyx_type_3src_9screening_9gap_ptest_GAP_Ptest) < 0) __PYX_ERR(0, 23, __pyx_L1_error)
- __pyx_ptype_3src_9screening_9gap_ptest_GAP_Ptest = &__pyx_type_3src_9screening_9gap_ptest_GAP_Ptest;
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s_GapTestAll, (PyObject *)&__pyx_type_3src_9screening_12gap_test_all_GapTestAll) < 0) __PYX_ERR(0, 21, __pyx_L1_error)
+ if (__Pyx_setup_reduce((PyObject*)&__pyx_type_3src_9screening_12gap_test_all_GapTestAll) < 0) __PYX_ERR(0, 21, __pyx_L1_error)
+ __pyx_ptype_3src_9screening_12gap_test_all_GapTestAll = &__pyx_type_3src_9screening_12gap_test_all_GapTestAll;
__Pyx_RefNannyFinishContext();
return 0;
__pyx_L1_error:;
@@ -4773,11 +4795,11 @@ static int __Pyx_modinit_function_import_code(void) {
#if PY_MAJOR_VERSION < 3
-__Pyx_PyMODINIT_FUNC initgap_ptest(void) CYTHON_SMALL_CODE; /*proto*/
-__Pyx_PyMODINIT_FUNC initgap_ptest(void)
+__Pyx_PyMODINIT_FUNC initgap_test_all(void) CYTHON_SMALL_CODE; /*proto*/
+__Pyx_PyMODINIT_FUNC initgap_test_all(void)
#else
-__Pyx_PyMODINIT_FUNC PyInit_gap_ptest(void) CYTHON_SMALL_CODE; /*proto*/
-__Pyx_PyMODINIT_FUNC PyInit_gap_ptest(void)
+__Pyx_PyMODINIT_FUNC PyInit_gap_test_all(void) CYTHON_SMALL_CODE; /*proto*/
+__Pyx_PyMODINIT_FUNC PyInit_gap_test_all(void)
#if CYTHON_PEP489_MULTI_PHASE_INIT
{
return PyModuleDef_Init(&__pyx_moduledef);
@@ -4844,7 +4866,7 @@ bad:
}
-static CYTHON_SMALL_CODE int __pyx_pymod_exec_gap_ptest(PyObject *__pyx_pyinit_module)
+static CYTHON_SMALL_CODE int __pyx_pymod_exec_gap_test_all(PyObject *__pyx_pyinit_module)
#endif
#endif
{
@@ -4857,7 +4879,7 @@ static CYTHON_SMALL_CODE int __pyx_pymod_exec_gap_ptest(PyObject *__pyx_pyinit_m
#if CYTHON_PEP489_MULTI_PHASE_INIT
if (__pyx_m) {
if (__pyx_m == __pyx_pyinit_module) return 0;
- PyErr_SetString(PyExc_RuntimeError, "Module 'gap_ptest' has already been imported. Re-initialisation is not supported.");
+ PyErr_SetString(PyExc_RuntimeError, "Module 'gap_test_all' has already been imported. Re-initialisation is not supported.");
return -1;
}
#elif PY_MAJOR_VERSION >= 3
@@ -4872,7 +4894,7 @@ if (!__Pyx_RefNanny) {
Py_FatalError("failed to import 'refnanny' module");
}
#endif
- __Pyx_RefNannySetupContext("__Pyx_PyMODINIT_FUNC PyInit_gap_ptest(void)", 0);
+ __Pyx_RefNannySetupContext("__Pyx_PyMODINIT_FUNC PyInit_gap_test_all(void)", 0);
if (__Pyx_check_binary_version() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
#ifdef __Pxy_PyFrame_Initialize_Offsets
__Pxy_PyFrame_Initialize_Offsets();
@@ -4909,7 +4931,7 @@ if (!__Pyx_RefNanny) {
Py_INCREF(__pyx_m);
#else
#if PY_MAJOR_VERSION < 3
- __pyx_m = Py_InitModule4("gap_ptest", __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
+ __pyx_m = Py_InitModule4("gap_test_all", __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
#else
__pyx_m = PyModule_Create(&__pyx_moduledef);
#endif
@@ -4927,14 +4949,14 @@ if (!__Pyx_RefNanny) {
#if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT)
if (__Pyx_init_sys_getdefaultencoding_params() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
#endif
- if (__pyx_module_is_main_src__screening__gap_ptest) {
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s_name, __pyx_n_s_main) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
+ if (__pyx_module_is_main_src__screening__gap_test_all) {
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s_name_2, __pyx_n_s_main) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
}
#if PY_MAJOR_VERSION >= 3
{
PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) __PYX_ERR(0, 1, __pyx_L1_error)
- if (!PyDict_GetItemString(modules, "src.screening.gap_ptest")) {
- if (unlikely(PyDict_SetItemString(modules, "src.screening.gap_ptest", __pyx_m) < 0)) __PYX_ERR(0, 1, __pyx_L1_error)
+ if (!PyDict_GetItemString(modules, "src.screening.gap_test_all")) {
+ if (unlikely(PyDict_SetItemString(modules, "src.screening.gap_test_all", __pyx_m) < 0)) __PYX_ERR(0, 1, __pyx_L1_error)
}
}
#endif
@@ -4955,7 +4977,7 @@ if (!__Pyx_RefNanny) {
if (__Pyx_patch_abc() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
#endif
- /* "src/screening/gap_ptest.pyx":4
+ /* "src/screening/gap_test_all.pyx":4
* # Based on https://cython.readthedocs.io/en/latest/src/tutorial/numpy.html
* # https://cython.readthedocs.io/en/latest/src/tutorial/memory_allocation.html
* import numpy as np # <<<<<<<<<<<<<<
@@ -4967,7 +4989,7 @@ if (!__Pyx_RefNanny) {
if (PyDict_SetItem(__pyx_d, __pyx_n_s_np, __pyx_t_1) < 0) __PYX_ERR(0, 4, __pyx_L1_error)
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "src/screening/gap_ptest.pyx":6
+ /* "src/screening/gap_test_all.pyx":6
* import numpy as np
*
* from src.screening.ascreening import AbstractGapScreening # <<<<<<<<<<<<<<
@@ -4988,7 +5010,7 @@ if (!__Pyx_RefNanny) {
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "src/screening/gap_ptest.pyx":1
+ /* "src/screening/gap_test_all.pyx":1
* # -*- coding: utf-8 -*- # <<<<<<<<<<<<<<
* # Based on https://cython.readthedocs.io/en/latest/src/tutorial/numpy.html
* # https://cython.readthedocs.io/en/latest/src/tutorial/memory_allocation.html
@@ -5014,11 +5036,11 @@ if (!__Pyx_RefNanny) {
__Pyx_XDECREF(__pyx_t_2);
if (__pyx_m) {
if (__pyx_d) {
- __Pyx_AddTraceback("init src.screening.gap_ptest", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("init src.screening.gap_test_all", __pyx_clineno, __pyx_lineno, __pyx_filename);
}
Py_CLEAR(__pyx_m);
} else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_ImportError, "init src.screening.gap_ptest");
+ PyErr_SetString(PyExc_ImportError, "init src.screening.gap_test_all");
}
__pyx_L0:;
__Pyx_RefNannyFinishContext();
@@ -5800,6 +5822,20 @@ fail:;
return -1;
}
+/* PyObjectSetAttrStr */
+ #if CYTHON_USE_TYPE_SLOTS
+static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value) {
+ PyTypeObject* tp = Py_TYPE(obj);
+ if (likely(tp->tp_setattro))
+ return tp->tp_setattro(obj, attr_name, value);
+#if PY_MAJOR_VERSION < 3
+ if (likely(tp->tp_setattr))
+ return tp->tp_setattr(obj, PyString_AS_STRING(attr_name), value);
+#endif
+ return PyObject_SetAttr(obj, attr_name, value);
+}
+#endif
+
/* PyErrFetchRestore */
#if CYTHON_FAST_THREAD_STATE
static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) {
@@ -6790,7 +6826,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, P
static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) {
int ret;
PyObject *name_attr;
- name_attr = __Pyx_PyObject_GetAttrStr(meth, __pyx_n_s_name);
+ name_attr = __Pyx_PyObject_GetAttrStr(meth, __pyx_n_s_name_2);
if (likely(name_attr)) {
ret = PyObject_RichCompareBool(name_attr, name, Py_EQ);
} else {
diff --git a/src/screening/gap_ptest.pyx b/src/screening/gap_test_all.pyx
similarity index 83%
rename from src/screening/gap_ptest.pyx
rename to src/screening/gap_test_all.pyx
index e8380faa1027988d0394f6094ffdc9f4b4d4ff7b..4bd697c7d95a6381e1e662a89ab1d818c566277b 100644
--- a/src/screening/gap_ptest.pyx
+++ b/src/screening/gap_test_all.pyx
@@ -18,9 +18,7 @@ from cpython.mem cimport PyMem_Malloc, PyMem_Realloc, PyMem_Free
ctypedef np.npy_bool bool_t
-#(AbstractGapScreening)
-
-cdef class GAP_Ptest:
+cdef class GapTestAll:
""" Generalized test
"""
@@ -47,22 +45,21 @@ cdef class GAP_Ptest:
# self.vec_cumsum_gammas = &buf[0]
+ self.name = "GAP test-all (cython)"
+
def __dealloc__(self):
PyMem_Free(self.vec_cumsum_gammas) # no-op if self.data is NULL
- def get_name(self):
- return "p-test cython"
-
-
@cython.boundscheck(False) # turn off bounds-checking for entire function
# @cython.wraparound(False) # turn off negative index wrapping for entire function
def apply_test(self,
np.ndarray[np.npy_double, ndim=1] Atcabs,
double gap,
double lbd,
- np.ndarray[np.npy_double, ndim=1] vec_gammas,
+ np.ndarray[np.npy_double, ndim=1] vec_gammas,
+ double coeff_dual_scaling =1.,
double offset_radius=0.,
np.ndarray[long, ndim=1] index=None
):
@@ -82,6 +79,11 @@ cdef class GAP_Ptest:
vec_gammas : np.ndarray
slope parameters
size [n,]
+ coeff_dual_scaling : positif float
+ If coeff_dual_scaling is not feasible, dual scaling factor
+ such taht vecu / coeff_dual_scaling os dual feasible
+ Here for code optimization purposes
+ Default value is 1. (vecu is feasible)
offset_radius : float
additive term added to the redius
default is 0
@@ -101,7 +103,9 @@ cdef class GAP_Ptest:
# all indexes below range from 1 to n (instead of 0 to n-1)
# in order to match the paper indexation rules
- cdef double radius = np.sqrt(2 * gap) + offset_radius
+ cdef double radius = coeff_dual_scaling * np.sqrt(2 * gap) + offset_radius
+ # cdef double lbd_aug = coeff_dual_scaling * lbd
+ cdef np.ndarray[np.npy_double, ndim=1] coeff_lbd_gamma = coeff_dual_scaling * lbd * vec_gammas
cdef int n = Atcabs.shape[0]
cdef int k, q, r
@@ -121,10 +125,10 @@ cdef class GAP_Ptest:
# 2. Precomputing quantities
cdef np.ndarray[np.npy_double, ndim=1] vec_f = np.cumsum(
- lbd * vec_gammas[::-1] - Atcabs[index[::-1]] - radius
+ coeff_lbd_gamma[::-1] - Atcabs[index[::-1]] - radius
)[::-1]
- cdef double best_bound_q = vec_f[0] - lbd * vec_gammas[0]
+ cdef double best_bound_q = vec_f[0] - coeff_lbd_gamma[0]
cdef double curr_bound_q = 0.
cdef double best_bound_p = vec_f[0]
cdef double curr_bound_p = 0.
@@ -140,7 +144,7 @@ cdef class GAP_Ptest:
vec_p_star[k] = vec_p_star[k-1]
# 1. Evaluate q*
- curr_bound_q = vec_f[k-1] - lbd * vec_gammas[k-1]
+ curr_bound_q = vec_f[k-1] - coeff_lbd_gamma[k-1]
if curr_bound_q > best_bound_q:
best_bound_q = curr_bound_q
vec_q_star[k] = k
@@ -155,7 +159,7 @@ cdef class GAP_Ptest:
p = vec_p_star[q]
# Evaluation of the threshold
- tau = vec_f[p-1] - vec_f[q-1] + (lbd * vec_gammas[q-1] - radius)
+ tau = vec_f[p-1] - vec_f[q-1] + (coeff_lbd_gamma[q-1] - radius)
# Test
if Atcabs[index[l-1]] >= tau:
diff --git a/src/screening/kappa_test.c b/src/screening/gap_test_p_1.c
similarity index 90%
rename from src/screening/kappa_test.c
rename to src/screening/gap_test_p_1.c
index 91c56fd81fc7564538165ca2cd96b8ea3a4c3881..ade654c8ab195b25ba9c2e7816c72fbd84394692 100644
--- a/src/screening/kappa_test.c
+++ b/src/screening/gap_test_p_1.c
@@ -4,12 +4,12 @@
{
"distutils": {
"depends": [],
- "name": "src.screening.kappa_test",
+ "name": "src.screening.gap_test_p_1",
"sources": [
- "src/screening/kappa_test.pyx"
+ "src/screening/gap_test_p_1.pyx"
]
},
- "module_name": "src.screening.kappa_test"
+ "module_name": "src.screening.gap_test_p_1"
}
END: Cython Metadata */
@@ -625,8 +625,8 @@ static CYTHON_INLINE float __PYX_NAN() {
#endif
#endif
-#define __PYX_HAVE__src__screening__kappa_test
-#define __PYX_HAVE_API__src__screening__kappa_test
+#define __PYX_HAVE__src__screening__gap_test_p_1
+#define __PYX_HAVE_API__src__screening__gap_test_p_1
/* Early includes */
#include <string.h>
#include <stdio.h>
@@ -868,7 +868,7 @@ static const char *__pyx_filename;
static const char *__pyx_f[] = {
- "src/screening/kappa_test.pyx",
+ "src/screening/gap_test_p_1.pyx",
"stringsource",
"venv/lib/python3.8/site-packages/numpy/__init__.pxd",
"venv/lib/python3.8/site-packages/Cython/Includes/cpython/type.pxd",
@@ -1099,14 +1099,14 @@ typedef npy_double __pyx_t_5numpy_double_t;
*/
typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
-/* "src/screening/kappa_test.pyx":16
+/* "src/screening/gap_test_p_1.pyx":16
* cimport cython
*
* ctypedef np.npy_bool bool_t # <<<<<<<<<<<<<<
*
* from cpython.mem cimport PyMem_Malloc, PyMem_Realloc, PyMem_Free
*/
-typedef npy_bool __pyx_t_3src_9screening_10kappa_test_bool_t;
+typedef npy_bool __pyx_t_3src_9screening_12gap_test_p_1_bool_t;
/* Declarations.proto */
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
@@ -1133,7 +1133,7 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do
/*--- Type declarations ---*/
-struct __pyx_obj_3src_9screening_10kappa_test_Kappa_test;
+struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne;
/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":729
* ctypedef npy_longdouble longdouble_t
@@ -1171,14 +1171,14 @@ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
*/
typedef npy_cdouble __pyx_t_5numpy_complex_t;
-/* "src/screening/kappa_test.pyx":23
+/* "src/screening/gap_test_p_1.pyx":23
* #(AbstractGapScreening)
*
- * cdef class Kappa_test: # <<<<<<<<<<<<<<
+ * cdef class GapTestPequalOne: # <<<<<<<<<<<<<<
* """ Generalized test
* """
*/
-struct __pyx_obj_3src_9screening_10kappa_test_Kappa_test {
+struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne {
PyObject_HEAD
double *vec_cumsum_gammas;
double *vec_kappa_q;
@@ -1394,6 +1394,15 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject
/* PyObjectCallOneArg.proto */
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg);
+/* PyObjectSetAttrStr.proto */
+#if CYTHON_USE_TYPE_SLOTS
+#define __Pyx_PyObject_DelAttrStr(o,n) __Pyx_PyObject_SetAttrStr(o, n, NULL)
+static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value);
+#else
+#define __Pyx_PyObject_DelAttrStr(o,n) PyObject_DelAttr(o,n)
+#define __Pyx_PyObject_SetAttrStr(o,n,v) PyObject_SetAttr(o,n,v)
+#endif
+
/* PyThreadStateGet.proto */
#if CYTHON_FAST_THREAD_STATE
#define __Pyx_PyThreadState_declare PyThreadState *__pyx_tstate;
@@ -1761,16 +1770,16 @@ static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0;
/* Module declarations from 'cython' */
-/* Module declarations from 'src.screening.kappa_test' */
-static PyTypeObject *__pyx_ptype_3src_9screening_10kappa_test_Kappa_test = 0;
+/* Module declarations from 'src.screening.gap_test_p_1' */
+static PyTypeObject *__pyx_ptype_3src_9screening_12gap_test_p_1_GapTestPequalOne = 0;
static __Pyx_TypeInfo __Pyx_TypeInfo_nn_npy_double = { "npy_double", NULL, sizeof(npy_double), { 0 }, 0, 'R', 0, 0 };
static __Pyx_TypeInfo __Pyx_TypeInfo_long = { "long", NULL, sizeof(long), { 0 }, 0, IS_UNSIGNED(long) ? 'U' : 'I', IS_UNSIGNED(long), 0 };
static __Pyx_TypeInfo __Pyx_TypeInfo_nn_npy_bool = { "npy_bool", NULL, sizeof(npy_bool), { 0 }, 0, IS_UNSIGNED(npy_bool) ? 'U' : 'I', IS_UNSIGNED(npy_bool), 0 };
-#define __Pyx_MODULE_NAME "src.screening.kappa_test"
-extern int __pyx_module_is_main_src__screening__kappa_test;
-int __pyx_module_is_main_src__screening__kappa_test = 0;
+#define __Pyx_MODULE_NAME "src.screening.gap_test_p_1"
+extern int __pyx_module_is_main_src__screening__gap_test_p_1;
+int __pyx_module_is_main_src__screening__gap_test_p_1 = 0;
-/* Implementation of 'src.screening.kappa_test' */
+/* Implementation of 'src.screening.gap_test_p_1' */
static PyObject *__pyx_builtin_range;
static PyObject *__pyx_builtin_TypeError;
static PyObject *__pyx_builtin_ImportError;
@@ -1778,7 +1787,7 @@ static const char __pyx_k_np[] = "np";
static const char __pyx_k_gap[] = "gap";
static const char __pyx_k_lbd[] = "lbd";
static const char __pyx_k_main[] = "__main__";
-static const char __pyx_k_name[] = "__name__";
+static const char __pyx_k_name[] = "name";
static const char __pyx_k_sqrt[] = "sqrt";
static const char __pyx_k_test[] = "__test__";
static const char __pyx_k_dtype[] = "dtype";
@@ -1790,20 +1799,22 @@ static const char __pyx_k_Atcabs[] = "Atcabs";
static const char __pyx_k_argmax[] = "argmax";
static const char __pyx_k_cumsum[] = "cumsum";
static const char __pyx_k_import[] = "__import__";
+static const char __pyx_k_name_2[] = "__name__";
static const char __pyx_k_reduce[] = "__reduce__";
static const char __pyx_k_argsort[] = "argsort";
static const char __pyx_k_getstate[] = "__getstate__";
static const char __pyx_k_setstate[] = "__setstate__";
static const char __pyx_k_TypeError[] = "TypeError";
static const char __pyx_k_reduce_ex[] = "__reduce_ex__";
-static const char __pyx_k_Kappa_test[] = "Kappa_test";
static const char __pyx_k_vec_gammas[] = "vec_gammas";
static const char __pyx_k_ImportError[] = "ImportError";
static const char __pyx_k_offset_radius[] = "offset_radius";
static const char __pyx_k_reduce_cython[] = "__reduce_cython__";
static const char __pyx_k_setstate_cython[] = "__setstate_cython__";
-static const char __pyx_k_kappa_test_cython[] = "kappa-test cython";
+static const char __pyx_k_GapTestPequalOne[] = "GapTestPequalOne";
static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback";
+static const char __pyx_k_coeff_dual_scaling[] = "coeff_dual_scaling";
+static const char __pyx_k_Gap_test_p_1_cython[] = "Gap test p=1 (cython)";
static const char __pyx_k_AbstractGapScreening[] = "AbstractGapScreening";
static const char __pyx_k_vec_coherence_function[] = "vec_coherence_function";
static const char __pyx_k_src_screening_ascreening[] = "src.screening.ascreening";
@@ -1812,22 +1823,24 @@ static const char __pyx_k_self_vec_cumsum_gammas_self_vec[] = "self.vec_cumsum_g
static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import";
static PyObject *__pyx_n_s_AbstractGapScreening;
static PyObject *__pyx_n_s_Atcabs;
+static PyObject *__pyx_n_s_GapTestPequalOne;
+static PyObject *__pyx_kp_s_Gap_test_p_1_cython;
static PyObject *__pyx_n_s_ImportError;
-static PyObject *__pyx_n_s_Kappa_test;
static PyObject *__pyx_n_s_TypeError;
static PyObject *__pyx_n_s_argmax;
static PyObject *__pyx_n_s_argsort;
static PyObject *__pyx_n_s_cline_in_traceback;
+static PyObject *__pyx_n_s_coeff_dual_scaling;
static PyObject *__pyx_n_s_cumsum;
static PyObject *__pyx_n_s_dtype;
static PyObject *__pyx_n_s_gap;
static PyObject *__pyx_n_s_getstate;
static PyObject *__pyx_n_s_import;
static PyObject *__pyx_n_s_index;
-static PyObject *__pyx_kp_s_kappa_test_cython;
static PyObject *__pyx_n_s_lbd;
static PyObject *__pyx_n_s_main;
static PyObject *__pyx_n_s_name;
+static PyObject *__pyx_n_s_name_2;
static PyObject *__pyx_n_s_np;
static PyObject *__pyx_n_s_numpy;
static PyObject *__pyx_kp_s_numpy_core_multiarray_failed_to;
@@ -1846,13 +1859,12 @@ static PyObject *__pyx_n_s_test;
static PyObject *__pyx_n_s_vec_coherence_function;
static PyObject *__pyx_n_s_vec_gammas;
static PyObject *__pyx_n_s_zeros;
-static int __pyx_pf_3src_9screening_10kappa_test_10Kappa_test___init__(struct __pyx_obj_3src_9screening_10kappa_test_Kappa_test *__pyx_v_self, PyArrayObject *__pyx_v_vec_gammas, PyArrayObject *__pyx_v_vec_coherence_function); /* proto */
-static void __pyx_pf_3src_9screening_10kappa_test_10Kappa_test_2__dealloc__(struct __pyx_obj_3src_9screening_10kappa_test_Kappa_test *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_3src_9screening_10kappa_test_10Kappa_test_4get_name(CYTHON_UNUSED struct __pyx_obj_3src_9screening_10kappa_test_Kappa_test *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_3src_9screening_10kappa_test_10Kappa_test_6apply_test(struct __pyx_obj_3src_9screening_10kappa_test_Kappa_test *__pyx_v_self, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_gap, double __pyx_v_lbd, CYTHON_UNUSED PyArrayObject *__pyx_v_vec_gammas, double __pyx_v_offset_radius, PyArrayObject *__pyx_v_index); /* proto */
-static PyObject *__pyx_pf_3src_9screening_10kappa_test_10Kappa_test_8__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_3src_9screening_10kappa_test_Kappa_test *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_3src_9screening_10kappa_test_10Kappa_test_10__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_3src_9screening_10kappa_test_Kappa_test *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
-static PyObject *__pyx_tp_new_3src_9screening_10kappa_test_Kappa_test(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
+static int __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self, PyArrayObject *__pyx_v_vec_gammas, PyArrayObject *__pyx_v_vec_coherence_function); /* proto */
+static void __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_2__dealloc__(struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4apply_test(struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_gap, double __pyx_v_lbd, CYTHON_UNUSED PyArrayObject *__pyx_v_vec_gammas, double __pyx_v_coeff_dual_scaling, double __pyx_v_offset_radius, PyArrayObject *__pyx_v_index); /* proto */
+static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_6__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_8__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
+static PyObject *__pyx_tp_new_3src_9screening_12gap_test_p_1_GapTestPequalOne(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_int_1;
static PyObject *__pyx_int_neg_1;
static PyObject *__pyx_slice_;
@@ -1863,7 +1875,7 @@ static PyObject *__pyx_tuple__5;
static PyObject *__pyx_tuple__6;
/* Late includes */
-/* "src/screening/kappa_test.pyx":38
+/* "src/screening/gap_test_p_1.pyx":38
* @cython.boundscheck(False) # turn off bounds-checking for entire function
* @cython.wraparound(False) # turn off negative index wrapping for entire function
* def __init__( # <<<<<<<<<<<<<<
@@ -1872,8 +1884,8 @@ static PyObject *__pyx_tuple__6;
*/
/* Python wrapper */
-static int __pyx_pw_3src_9screening_10kappa_test_10Kappa_test_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_3src_9screening_10kappa_test_10Kappa_test_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static int __pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyArrayObject *__pyx_v_vec_gammas = 0;
PyArrayObject *__pyx_v_vec_coherence_function = 0;
int __pyx_lineno = 0;
@@ -1924,13 +1936,13 @@ static int __pyx_pw_3src_9screening_10kappa_test_10Kappa_test_1__init__(PyObject
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("__init__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 38, __pyx_L3_error)
__pyx_L3_error:;
- __Pyx_AddTraceback("src.screening.kappa_test.Kappa_test.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("src.screening.gap_test_p_1.GapTestPequalOne.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_vec_gammas), __pyx_ptype_5numpy_ndarray, 1, "vec_gammas", 0))) __PYX_ERR(0, 40, __pyx_L1_error)
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_vec_coherence_function), __pyx_ptype_5numpy_ndarray, 1, "vec_coherence_function", 0))) __PYX_ERR(0, 41, __pyx_L1_error)
- __pyx_r = __pyx_pf_3src_9screening_10kappa_test_10Kappa_test___init__(((struct __pyx_obj_3src_9screening_10kappa_test_Kappa_test *)__pyx_v_self), __pyx_v_vec_gammas, __pyx_v_vec_coherence_function);
+ __pyx_r = __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(((struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *)__pyx_v_self), __pyx_v_vec_gammas, __pyx_v_vec_coherence_function);
/* function exit code */
goto __pyx_L0;
@@ -1941,7 +1953,7 @@ static int __pyx_pw_3src_9screening_10kappa_test_10Kappa_test_1__init__(PyObject
return __pyx_r;
}
-static int __pyx_pf_3src_9screening_10kappa_test_10Kappa_test___init__(struct __pyx_obj_3src_9screening_10kappa_test_Kappa_test *__pyx_v_self, PyArrayObject *__pyx_v_vec_gammas, PyArrayObject *__pyx_v_vec_coherence_function) {
+static int __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self, PyArrayObject *__pyx_v_vec_gammas, PyArrayObject *__pyx_v_vec_coherence_function) {
int __pyx_v_n;
int __pyx_v_i;
__Pyx_LocalBuf_ND __pyx_pybuffernd_vec_coherence_function;
@@ -1982,7 +1994,7 @@ static int __pyx_pf_3src_9screening_10kappa_test_10Kappa_test___init__(struct __
}
__pyx_pybuffernd_vec_coherence_function.diminfo[0].strides = __pyx_pybuffernd_vec_coherence_function.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_vec_coherence_function.diminfo[0].shape = __pyx_pybuffernd_vec_coherence_function.rcbuffer->pybuffer.shape[0];
- /* "src/screening/kappa_test.pyx":44
+ /* "src/screening/gap_test_p_1.pyx":44
* ):
*
* cdef int n = vec_gammas.shape[0] # <<<<<<<<<<<<<<
@@ -1991,7 +2003,7 @@ static int __pyx_pf_3src_9screening_10kappa_test_10Kappa_test___init__(struct __
*/
__pyx_v_n = (__pyx_v_vec_gammas->dimensions[0]);
- /* "src/screening/kappa_test.pyx":56
+ /* "src/screening/gap_test_p_1.pyx":56
* # self.vec_kappa_q = &buf2[0]
*
* self.vec_cumsum_gammas = <double*> PyMem_Malloc(n * sizeof(double)) # <<<<<<<<<<<<<<
@@ -2000,7 +2012,7 @@ static int __pyx_pf_3src_9screening_10kappa_test_10Kappa_test___init__(struct __
*/
__pyx_v_self->vec_cumsum_gammas = ((double *)PyMem_Malloc((__pyx_v_n * (sizeof(double)))));
- /* "src/screening/kappa_test.pyx":57
+ /* "src/screening/gap_test_p_1.pyx":57
*
* self.vec_cumsum_gammas = <double*> PyMem_Malloc(n * sizeof(double))
* self.vec_cumsum_gammas[0] = vec_gammas[0] # <<<<<<<<<<<<<<
@@ -2010,7 +2022,7 @@ static int __pyx_pf_3src_9screening_10kappa_test_10Kappa_test___init__(struct __
__pyx_t_1 = 0;
(__pyx_v_self->vec_cumsum_gammas[0]) = (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_gammas.rcbuffer->pybuffer.buf, __pyx_t_1, __pyx_pybuffernd_vec_gammas.diminfo[0].strides));
- /* "src/screening/kappa_test.pyx":59
+ /* "src/screening/gap_test_p_1.pyx":59
* self.vec_cumsum_gammas[0] = vec_gammas[0]
*
* self.vec_kappa_q = <double*> PyMem_Malloc(n * sizeof(double)) # <<<<<<<<<<<<<<
@@ -2019,7 +2031,7 @@ static int __pyx_pf_3src_9screening_10kappa_test_10Kappa_test___init__(struct __
*/
__pyx_v_self->vec_kappa_q = ((double *)PyMem_Malloc((__pyx_v_n * (sizeof(double)))));
- /* "src/screening/kappa_test.pyx":61
+ /* "src/screening/gap_test_p_1.pyx":61
* self.vec_kappa_q = <double*> PyMem_Malloc(n * sizeof(double))
*
* cdef int i = 0 # <<<<<<<<<<<<<<
@@ -2028,7 +2040,7 @@ static int __pyx_pf_3src_9screening_10kappa_test_10Kappa_test___init__(struct __
*/
__pyx_v_i = 0;
- /* "src/screening/kappa_test.pyx":62
+ /* "src/screening/gap_test_p_1.pyx":62
*
* cdef int i = 0
* for i in range(1, n): # <<<<<<<<<<<<<<
@@ -2040,7 +2052,7 @@ static int __pyx_pf_3src_9screening_10kappa_test_10Kappa_test___init__(struct __
for (__pyx_t_4 = 1; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
__pyx_v_i = __pyx_t_4;
- /* "src/screening/kappa_test.pyx":63
+ /* "src/screening/gap_test_p_1.pyx":63
* cdef int i = 0
* for i in range(1, n):
* self.vec_cumsum_gammas[i] = self.vec_cumsum_gammas[i-1] + vec_gammas[i] # <<<<<<<<<<<<<<
@@ -2051,7 +2063,7 @@ static int __pyx_pf_3src_9screening_10kappa_test_10Kappa_test___init__(struct __
(__pyx_v_self->vec_cumsum_gammas[__pyx_v_i]) = ((__pyx_v_self->vec_cumsum_gammas[(__pyx_v_i - 1)]) + (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_gammas.rcbuffer->pybuffer.buf, __pyx_t_1, __pyx_pybuffernd_vec_gammas.diminfo[0].strides)));
}
- /* "src/screening/kappa_test.pyx":65
+ /* "src/screening/gap_test_p_1.pyx":65
* self.vec_cumsum_gammas[i] = self.vec_cumsum_gammas[i-1] + vec_gammas[i]
*
* for i in range(n): # <<<<<<<<<<<<<<
@@ -2063,7 +2075,7 @@ static int __pyx_pf_3src_9screening_10kappa_test_10Kappa_test___init__(struct __
for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
__pyx_v_i = __pyx_t_4;
- /* "src/screening/kappa_test.pyx":66
+ /* "src/screening/gap_test_p_1.pyx":66
*
* for i in range(n):
* self.vec_kappa_q[i] = np.sqrt( # <<<<<<<<<<<<<<
@@ -2076,7 +2088,7 @@ static int __pyx_pf_3src_9screening_10kappa_test_10Kappa_test___init__(struct __
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "src/screening/kappa_test.pyx":67
+ /* "src/screening/gap_test_p_1.pyx":67
* for i in range(n):
* self.vec_kappa_q[i] = np.sqrt(
* (1. + vec_coherence_function[i]) * (i + 1.) # <<<<<<<<<<<<<<
@@ -2103,7 +2115,7 @@ static int __pyx_pf_3src_9screening_10kappa_test_10Kappa_test___init__(struct __
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- /* "src/screening/kappa_test.pyx":66
+ /* "src/screening/gap_test_p_1.pyx":66
*
* for i in range(n):
* self.vec_kappa_q[i] = np.sqrt( # <<<<<<<<<<<<<<
@@ -2115,7 +2127,16 @@ static int __pyx_pf_3src_9screening_10kappa_test_10Kappa_test___init__(struct __
(__pyx_v_self->vec_kappa_q[__pyx_v_i]) = __pyx_t_9;
}
- /* "src/screening/kappa_test.pyx":38
+ /* "src/screening/gap_test_p_1.pyx":75
+ * # ).copy()
+ *
+ * self.name = "Gap test p=1 (cython)" # <<<<<<<<<<<<<<
+ *
+ *
+ */
+ if (__Pyx_PyObject_SetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_name, __pyx_kp_s_Gap_test_p_1_cython) < 0) __PYX_ERR(0, 75, __pyx_L1_error)
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* @cython.boundscheck(False) # turn off bounds-checking for entire function
* @cython.wraparound(False) # turn off negative index wrapping for entire function
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__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_vec_coherence_function.rcbuffer->pybuffer);
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_vec_gammas.rcbuffer->pybuffer);
__Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);}
- __Pyx_AddTraceback("src.screening.kappa_test.Kappa_test.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("src.screening.gap_test_p_1.GapTestPequalOne.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
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__pyx_L0:;
@@ -2149,7 +2170,7 @@ static int __pyx_pf_3src_9screening_10kappa_test_10Kappa_test___init__(struct __
return __pyx_r;
}
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*
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*/
/* Python wrapper */
-static void __pyx_pw_3src_9screening_10kappa_test_10Kappa_test_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pw_3src_9screening_10kappa_test_10Kappa_test_3__dealloc__(PyObject *__pyx_v_self) {
+static void __pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_3__dealloc__(PyObject *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
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+ __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_2__dealloc__(((struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *)__pyx_v_self));
/* function exit code */
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+static void __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_2__dealloc__(struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__dealloc__", 0);
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* def __dealloc__(self):
* PyMem_Free(self.vec_cumsum_gammas) # no-op if self.data is NULL # <<<<<<<<<<<<<<
@@ -2181,16 +2202,16 @@ static void __pyx_pf_3src_9screening_10kappa_test_10Kappa_test_2__dealloc__(stru
*/
PyMem_Free(__pyx_v_self->vec_cumsum_gammas);
- /* "src/screening/kappa_test.pyx":78
+ /* "src/screening/gap_test_p_1.pyx":80
* def __dealloc__(self):
* PyMem_Free(self.vec_cumsum_gammas) # no-op if self.data is NULL
* PyMem_Free(self.vec_kappa_q) # no-op if self.data is NULL # <<<<<<<<<<<<<<
*
- * def get_name(self):
+ *
*/
PyMem_Free(__pyx_v_self->vec_kappa_q);
- /* "src/screening/kappa_test.pyx":76
+ /* "src/screening/gap_test_p_1.pyx":78
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*
* def __dealloc__(self): # <<<<<<<<<<<<<<
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__Pyx_RefNannyFinishContext();
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- *
- */
-
-/* Python wrapper */
-static PyObject *__pyx_pw_3src_9screening_10kappa_test_10Kappa_test_5get_name(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static PyObject *__pyx_pw_3src_9screening_10kappa_test_10Kappa_test_5get_name(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
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- /* function exit code */
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
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-static PyObject *__pyx_pf_3src_9screening_10kappa_test_10Kappa_test_4get_name(CYTHON_UNUSED struct __pyx_obj_3src_9screening_10kappa_test_Kappa_test *__pyx_v_self) {
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- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("get_name", 0);
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- /* "src/screening/kappa_test.pyx":81
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- *
- *
- */
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_kp_s_kappa_test_cython);
- __pyx_r = __pyx_kp_s_kappa_test_cython;
- goto __pyx_L0;
-
- /* "src/screening/kappa_test.pyx":80
- * PyMem_Free(self.vec_kappa_q) # no-op if self.data is NULL
- *
- * def get_name(self): # <<<<<<<<<<<<<<
- * return "kappa-test cython"
- *
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-
- /* function exit code */
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
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-/* "src/screening/kappa_test.pyx":86
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* @cython.wraparound(False) # turn off negative index wrapping for entire function
* def apply_test(self, # <<<<<<<<<<<<<<
@@ -2264,13 +2232,14 @@ static PyObject *__pyx_pf_3src_9screening_10kappa_test_10Kappa_test_4get_name(CY
*/
/* Python wrapper */
-static PyObject *__pyx_pw_3src_9screening_10kappa_test_10Kappa_test_7apply_test(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_3src_9screening_10kappa_test_10Kappa_test_6apply_test[] = " Apply the Gap safe sphere screening test\n\n Implementation of the safe screening test\n \n Parameters\n ----------\n Atcabs : np.ndarray\n vector matA.T @ vecc where vec is dual admissible in absolute value\n size [n]\n gap : positive float\n duality gap\n lbd : positive float\n regularization parameters\n vec_gammas : np.ndarray\n slope parameters\n size [n,]\n offset_radius : float\n additive term added to the redius\n default is 0\n index : np.ndarray\n Array of indices that sort Atu in absolute value\n default is None\n \n Returns\n -------\n calI_screen : np.ndarray\n vector of boolean\n True if screening test passes and False otherwise\n size [n,]\n ";
-static PyObject *__pyx_pw_3src_9screening_10kappa_test_10Kappa_test_7apply_test(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_5apply_test(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4apply_test[] = " Apply the Gap safe sphere screening test\n\n Implementation of the safe screening test\n \n Parameters\n ----------\n Atcabs : np.ndarray\n vector matA.T @ vecc where vec is dual admissible in absolute value\n size [n]\n gap : positive float\n duality gap\n lbd : positive float\n regularization parameters\n vec_gammas : np.ndarray\n slope parameters\n size [n,]\n vec_gammas : np.ndarray\n slope parameters\n size [n,]\n coeff_dual_scaling : positif float\n If coeff_dual_scaling is not feasible, dual scaling factor\n such taht vecu / coeff_dual_scaling os dual feasible\n Here for code optimization purposes\n Default value is 1. (vecu is feasible)\n offset_radius : float\n additive term added to the redius\n default is 0\n index : np.ndarray\n Array of indices that sort Atu in absolute value\n default is None\n \n Returns\n -------\n calI_screen : np.ndarray\n vector of boolean\n True if screening test passes and False otherwise\n size [n,]\n ";
+static PyObject *__pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_5apply_test(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyArrayObject *__pyx_v_Atcabs = 0;
double __pyx_v_gap;
double __pyx_v_lbd;
CYTHON_UNUSED PyArrayObject *__pyx_v_vec_gammas = 0;
+ double __pyx_v_coeff_dual_scaling;
double __pyx_v_offset_radius;
PyArrayObject *__pyx_v_index = 0;
int __pyx_lineno = 0;
@@ -2280,21 +2249,23 @@ static PyObject *__pyx_pw_3src_9screening_10kappa_test_10Kappa_test_7apply_test(
__Pyx_RefNannyDeclarations
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- PyObject* values[6] = {0,0,0,0,0,0};
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_Atcabs,&__pyx_n_s_gap,&__pyx_n_s_lbd,&__pyx_n_s_vec_gammas,&__pyx_n_s_coeff_dual_scaling,&__pyx_n_s_offset_radius,&__pyx_n_s_index,0};
+ PyObject* values[7] = {0,0,0,0,0,0,0};
- /* "src/screening/kappa_test.pyx":92
- * np.ndarray[np.npy_double, ndim=1] vec_gammas,
+ /* "src/screening/gap_test_p_1.pyx":92
+ * double coeff_dual_scaling = 1.,
* double offset_radius=0.,
* np.ndarray[long, ndim=1] index=None # <<<<<<<<<<<<<<
* ):
* """ Apply the Gap safe sphere screening test
*/
- values[5] = (PyObject *)((PyArrayObject *)Py_None);
+ values[6] = (PyObject *)((PyArrayObject *)Py_None);
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
switch (pos_args) {
+ case 7: values[6] = PyTuple_GET_ITEM(__pyx_args, 6);
+ CYTHON_FALLTHROUGH;
case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
CYTHON_FALLTHROUGH;
case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
@@ -2319,38 +2290,46 @@ static PyObject *__pyx_pw_3src_9screening_10kappa_test_10Kappa_test_7apply_test(
case 1:
if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_gap)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("apply_test", 0, 4, 6, 1); __PYX_ERR(0, 86, __pyx_L3_error)
+ __Pyx_RaiseArgtupleInvalid("apply_test", 0, 4, 7, 1); __PYX_ERR(0, 85, __pyx_L3_error)
}
CYTHON_FALLTHROUGH;
case 2:
if (likely((values[2] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_lbd)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("apply_test", 0, 4, 6, 2); __PYX_ERR(0, 86, __pyx_L3_error)
+ __Pyx_RaiseArgtupleInvalid("apply_test", 0, 4, 7, 2); __PYX_ERR(0, 85, __pyx_L3_error)
}
CYTHON_FALLTHROUGH;
case 3:
if (likely((values[3] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_vec_gammas)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("apply_test", 0, 4, 6, 3); __PYX_ERR(0, 86, __pyx_L3_error)
+ __Pyx_RaiseArgtupleInvalid("apply_test", 0, 4, 7, 3); __PYX_ERR(0, 85, __pyx_L3_error)
}
CYTHON_FALLTHROUGH;
case 4:
if (kw_args > 0) {
- PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_offset_radius);
+ PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_coeff_dual_scaling);
if (value) { values[4] = value; kw_args--; }
}
CYTHON_FALLTHROUGH;
case 5:
if (kw_args > 0) {
- PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_index);
+ PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_offset_radius);
if (value) { values[5] = value; kw_args--; }
}
+ CYTHON_FALLTHROUGH;
+ case 6:
+ if (kw_args > 0) {
+ PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_index);
+ if (value) { values[6] = value; kw_args--; }
+ }
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "apply_test") < 0)) __PYX_ERR(0, 86, __pyx_L3_error)
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "apply_test") < 0)) __PYX_ERR(0, 85, __pyx_L3_error)
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
+ case 7: values[6] = PyTuple_GET_ITEM(__pyx_args, 6);
+ CYTHON_FALLTHROUGH;
case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
CYTHON_FALLTHROUGH;
case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
@@ -2364,30 +2343,35 @@ static PyObject *__pyx_pw_3src_9screening_10kappa_test_10Kappa_test_7apply_test(
}
}
__pyx_v_Atcabs = ((PyArrayObject *)values[0]);
- __pyx_v_gap = __pyx_PyFloat_AsDouble(values[1]); if (unlikely((__pyx_v_gap == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 88, __pyx_L3_error)
- __pyx_v_lbd = __pyx_PyFloat_AsDouble(values[2]); if (unlikely((__pyx_v_lbd == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 89, __pyx_L3_error)
+ __pyx_v_gap = __pyx_PyFloat_AsDouble(values[1]); if (unlikely((__pyx_v_gap == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 87, __pyx_L3_error)
+ __pyx_v_lbd = __pyx_PyFloat_AsDouble(values[2]); if (unlikely((__pyx_v_lbd == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 88, __pyx_L3_error)
__pyx_v_vec_gammas = ((PyArrayObject *)values[3]);
if (values[4]) {
- __pyx_v_offset_radius = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_offset_radius == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 91, __pyx_L3_error)
+ __pyx_v_coeff_dual_scaling = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_coeff_dual_scaling == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 90, __pyx_L3_error)
+ } else {
+ __pyx_v_coeff_dual_scaling = ((double)1.);
+ }
+ if (values[5]) {
+ __pyx_v_offset_radius = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_offset_radius == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 91, __pyx_L3_error)
} else {
__pyx_v_offset_radius = ((double)0.);
}
- __pyx_v_index = ((PyArrayObject *)values[5]);
+ __pyx_v_index = ((PyArrayObject *)values[6]);
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("apply_test", 0, 4, 6, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 86, __pyx_L3_error)
+ __Pyx_RaiseArgtupleInvalid("apply_test", 0, 4, 7, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 85, __pyx_L3_error)
__pyx_L3_error:;
- __Pyx_AddTraceback("src.screening.kappa_test.Kappa_test.apply_test", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("src.screening.gap_test_p_1.GapTestPequalOne.apply_test", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_Atcabs), __pyx_ptype_5numpy_ndarray, 1, "Atcabs", 0))) __PYX_ERR(0, 87, __pyx_L1_error)
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_vec_gammas), __pyx_ptype_5numpy_ndarray, 1, "vec_gammas", 0))) __PYX_ERR(0, 90, __pyx_L1_error)
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_Atcabs), __pyx_ptype_5numpy_ndarray, 1, "Atcabs", 0))) __PYX_ERR(0, 86, __pyx_L1_error)
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_vec_gammas), __pyx_ptype_5numpy_ndarray, 1, "vec_gammas", 0))) __PYX_ERR(0, 89, __pyx_L1_error)
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_index), __pyx_ptype_5numpy_ndarray, 1, "index", 0))) __PYX_ERR(0, 92, __pyx_L1_error)
- __pyx_r = __pyx_pf_3src_9screening_10kappa_test_10Kappa_test_6apply_test(((struct __pyx_obj_3src_9screening_10kappa_test_Kappa_test *)__pyx_v_self), __pyx_v_Atcabs, __pyx_v_gap, __pyx_v_lbd, __pyx_v_vec_gammas, __pyx_v_offset_radius, __pyx_v_index);
+ __pyx_r = __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4apply_test(((struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *)__pyx_v_self), __pyx_v_Atcabs, __pyx_v_gap, __pyx_v_lbd, __pyx_v_vec_gammas, __pyx_v_coeff_dual_scaling, __pyx_v_offset_radius, __pyx_v_index);
- /* "src/screening/kappa_test.pyx":86
+ /* "src/screening/gap_test_p_1.pyx":85
* @cython.boundscheck(False) # turn off bounds-checking for entire function
* @cython.wraparound(False) # turn off negative index wrapping for entire function
* def apply_test(self, # <<<<<<<<<<<<<<
@@ -2404,13 +2388,14 @@ static PyObject *__pyx_pw_3src_9screening_10kappa_test_10Kappa_test_7apply_test(
return __pyx_r;
}
-static PyObject *__pyx_pf_3src_9screening_10kappa_test_10Kappa_test_6apply_test(struct __pyx_obj_3src_9screening_10kappa_test_Kappa_test *__pyx_v_self, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_gap, double __pyx_v_lbd, CYTHON_UNUSED PyArrayObject *__pyx_v_vec_gammas, double __pyx_v_offset_radius, PyArrayObject *__pyx_v_index) {
+static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4apply_test(struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_gap, double __pyx_v_lbd, CYTHON_UNUSED PyArrayObject *__pyx_v_vec_gammas, double __pyx_v_coeff_dual_scaling, double __pyx_v_offset_radius, PyArrayObject *__pyx_v_index) {
int __pyx_v_n;
int __pyx_v_q;
int __pyx_v_l_q;
int __pyx_v_l_min;
double __pyx_v_bound;
double __pyx_v_radius;
+ double __pyx_v_coeff_lbd;
PyArrayObject *__pyx_v_sigmas = 0;
PyArrayObject *__pyx_v_calI_screen = 0;
__Pyx_LocalBuf_ND __pyx_pybuffernd_Atcabs;
@@ -2429,19 +2414,19 @@ static PyObject *__pyx_pf_3src_9screening_10kappa_test_10Kappa_test_6apply_test(
PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
PyObject *__pyx_t_4 = NULL;
- double __pyx_t_5;
- PyArrayObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_5 = NULL;
+ double __pyx_t_6;
PyArrayObject *__pyx_t_7 = NULL;
- int __pyx_t_8;
+ PyArrayObject *__pyx_t_8 = NULL;
int __pyx_t_9;
- PyArrayObject *__pyx_t_10 = NULL;
- int __pyx_t_11;
- PyObject *__pyx_t_12 = NULL;
+ int __pyx_t_10;
+ PyArrayObject *__pyx_t_11 = NULL;
+ int __pyx_t_12;
PyObject *__pyx_t_13 = NULL;
PyObject *__pyx_t_14 = NULL;
- Py_ssize_t __pyx_t_15;
+ PyObject *__pyx_t_15 = NULL;
Py_ssize_t __pyx_t_16;
- PyObject *__pyx_t_17 = NULL;
+ Py_ssize_t __pyx_t_17;
PyObject *__pyx_t_18 = NULL;
int __pyx_t_19;
int __pyx_t_20;
@@ -2473,21 +2458,21 @@ static PyObject *__pyx_pf_3src_9screening_10kappa_test_10Kappa_test_6apply_test(
__pyx_pybuffernd_index.rcbuffer = &__pyx_pybuffer_index;
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+static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_8__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
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+static PyObject *__pyx_tp_new_3src_9screening_12gap_test_p_1_GapTestPequalOne(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
PyObject *o;
if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
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return o;
}
-static void __pyx_tp_dealloc_3src_9screening_10kappa_test_Kappa_test(PyObject *o) {
+static void __pyx_tp_dealloc_3src_9screening_12gap_test_p_1_GapTestPequalOne(PyObject *o) {
#if CYTHON_USE_TP_FINALIZE
if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) {
if (PyObject_CallFinalizerFromDealloc(o)) return;
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PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
__Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1);
- __pyx_pw_3src_9screening_10kappa_test_10Kappa_test_3__dealloc__(o);
+ __pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_3__dealloc__(o);
__Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1);
PyErr_Restore(etype, eval, etb);
}
(*Py_TYPE(o)->tp_free)(o);
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- {"__reduce_cython__", (PyCFunction)__pyx_pw_3src_9screening_10kappa_test_10Kappa_test_9__reduce_cython__, METH_NOARGS, 0},
- {"__setstate_cython__", (PyCFunction)__pyx_pw_3src_9screening_10kappa_test_10Kappa_test_11__setstate_cython__, METH_O, 0},
+static PyMethodDef __pyx_methods_3src_9screening_12gap_test_p_1_GapTestPequalOne[] = {
+ {"apply_test", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_5apply_test, METH_VARARGS|METH_KEYWORDS, __pyx_doc_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4apply_test},
+ {"__reduce_cython__", (PyCFunction)__pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_7__reduce_cython__, METH_NOARGS, 0},
+ {"__setstate_cython__", (PyCFunction)__pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_9__setstate_cython__, METH_O, 0},
{0, 0, 0, 0}
};
-static PyTypeObject __pyx_type_3src_9screening_10kappa_test_Kappa_test = {
+static PyTypeObject __pyx_type_3src_9screening_12gap_test_p_1_GapTestPequalOne = {
PyVarObject_HEAD_INIT(0, 0)
- "src.screening.kappa_test.Kappa_test", /*tp_name*/
- sizeof(struct __pyx_obj_3src_9screening_10kappa_test_Kappa_test), /*tp_basicsize*/
+ "src.screening.gap_test_p_1.GapTestPequalOne", /*tp_name*/
+ sizeof(struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_3src_9screening_10kappa_test_Kappa_test, /*tp_dealloc*/
+ __pyx_tp_dealloc_3src_9screening_12gap_test_p_1_GapTestPequalOne, /*tp_dealloc*/
#if PY_VERSION_HEX < 0x030800b4
0, /*tp_print*/
#endif
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0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_3src_9screening_10kappa_test_Kappa_test, /*tp_methods*/
+ __pyx_methods_3src_9screening_12gap_test_p_1_GapTestPequalOne, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
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0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pw_3src_9screening_10kappa_test_10Kappa_test_1__init__, /*tp_init*/
+ __pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_1__init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_3src_9screening_10kappa_test_Kappa_test, /*tp_new*/
+ __pyx_tp_new_3src_9screening_12gap_test_p_1_GapTestPequalOne, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
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#if CYTHON_PEP489_MULTI_PHASE_INIT
static PyObject* __pyx_pymod_create(PyObject *spec, PyModuleDef *def); /*proto*/
-static int __pyx_pymod_exec_kappa_test(PyObject* module); /*proto*/
+static int __pyx_pymod_exec_gap_test_p_1(PyObject* module); /*proto*/
static PyModuleDef_Slot __pyx_moduledef_slots[] = {
{Py_mod_create, (void*)__pyx_pymod_create},
- {Py_mod_exec, (void*)__pyx_pymod_exec_kappa_test},
+ {Py_mod_exec, (void*)__pyx_pymod_exec_gap_test_p_1},
{0, NULL}
};
#endif
static struct PyModuleDef __pyx_moduledef = {
PyModuleDef_HEAD_INIT,
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+ "gap_test_p_1",
0, /* m_doc */
#if CYTHON_PEP489_MULTI_PHASE_INIT
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{&__pyx_n_s_Atcabs, __pyx_k_Atcabs, sizeof(__pyx_k_Atcabs), 0, 0, 1, 1},
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* # Cdric' notations compliant
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- __pyx_type_3src_9screening_10kappa_test_Kappa_test.tp_getattro = __Pyx_PyObject_GenericGetAttr;
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+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s_GapTestPequalOne, (PyObject *)&__pyx_type_3src_9screening_12gap_test_p_1_GapTestPequalOne) < 0) __PYX_ERR(0, 23, __pyx_L1_error)
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@@ -4526,11 +4527,11 @@ static int __Pyx_modinit_function_import_code(void) {
#if PY_MAJOR_VERSION < 3
-__Pyx_PyMODINIT_FUNC initkappa_test(void) CYTHON_SMALL_CODE; /*proto*/
-__Pyx_PyMODINIT_FUNC initkappa_test(void)
+__Pyx_PyMODINIT_FUNC initgap_test_p_1(void) CYTHON_SMALL_CODE; /*proto*/
+__Pyx_PyMODINIT_FUNC initgap_test_p_1(void)
#else
-__Pyx_PyMODINIT_FUNC PyInit_kappa_test(void) CYTHON_SMALL_CODE; /*proto*/
-__Pyx_PyMODINIT_FUNC PyInit_kappa_test(void)
+__Pyx_PyMODINIT_FUNC PyInit_gap_test_p_1(void) CYTHON_SMALL_CODE; /*proto*/
+__Pyx_PyMODINIT_FUNC PyInit_gap_test_p_1(void)
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{
return PyModuleDef_Init(&__pyx_moduledef);
@@ -4597,7 +4598,7 @@ bad:
}
-static CYTHON_SMALL_CODE int __pyx_pymod_exec_kappa_test(PyObject *__pyx_pyinit_module)
+static CYTHON_SMALL_CODE int __pyx_pymod_exec_gap_test_p_1(PyObject *__pyx_pyinit_module)
#endif
#endif
{
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#if CYTHON_PEP489_MULTI_PHASE_INIT
if (__pyx_m) {
if (__pyx_m == __pyx_pyinit_module) return 0;
- PyErr_SetString(PyExc_RuntimeError, "Module 'kappa_test' has already been imported. Re-initialisation is not supported.");
+ PyErr_SetString(PyExc_RuntimeError, "Module 'gap_test_p_1' has already been imported. Re-initialisation is not supported.");
return -1;
}
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Py_FatalError("failed to import 'refnanny' module");
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Py_INCREF(__pyx_m);
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- __pyx_m = Py_InitModule4("kappa_test", __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
+ __pyx_m = Py_InitModule4("gap_test_p_1", __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
#else
__pyx_m = PyModule_Create(&__pyx_moduledef);
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- if (PyObject_SetAttr(__pyx_m, __pyx_n_s_name, __pyx_n_s_main) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
+ if (__pyx_module_is_main_src__screening__gap_test_p_1) {
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s_name_2, __pyx_n_s_main) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
}
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{
PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) __PYX_ERR(0, 1, __pyx_L1_error)
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- if (unlikely(PyDict_SetItemString(modules, "src.screening.kappa_test", __pyx_m) < 0)) __PYX_ERR(0, 1, __pyx_L1_error)
+ if (!PyDict_GetItemString(modules, "src.screening.gap_test_p_1")) {
+ if (unlikely(PyDict_SetItemString(modules, "src.screening.gap_test_p_1", __pyx_m) < 0)) __PYX_ERR(0, 1, __pyx_L1_error)
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if (__Pyx_patch_abc() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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- /* "src/screening/kappa_test.pyx":3
+ /* "src/screening/gap_test_p_1.pyx":3
* # -*- coding: utf-8 -*-
* # Based on https://cython.readthedocs.io/en/latest/src/tutorial/numpy.html
* import numpy as np # <<<<<<<<<<<<<<
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "src/screening/kappa_test.pyx":5
+ /* "src/screening/gap_test_p_1.pyx":5
* import numpy as np
*
* from src.screening.ascreening import AbstractGapScreening # <<<<<<<<<<<<<<
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__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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+ /* "src/screening/gap_test_p_1.pyx":1
* # -*- coding: utf-8 -*- # <<<<<<<<<<<<<<
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* import numpy as np
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__Pyx_XDECREF(__pyx_t_2);
if (__pyx_m) {
if (__pyx_d) {
- __Pyx_AddTraceback("init src.screening.kappa_test", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("init src.screening.gap_test_p_1", __pyx_clineno, __pyx_lineno, __pyx_filename);
}
Py_CLEAR(__pyx_m);
} else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_ImportError, "init src.screening.kappa_test");
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__Pyx_RefNannyFinishContext();
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}
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+/* PyObjectSetAttrStr */
+ #if CYTHON_USE_TYPE_SLOTS
+static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value) {
+ PyTypeObject* tp = Py_TYPE(obj);
+ if (likely(tp->tp_setattro))
+ return tp->tp_setattro(obj, attr_name, value);
+#if PY_MAJOR_VERSION < 3
+ if (likely(tp->tp_setattr))
+ return tp->tp_setattr(obj, PyString_AS_STRING(attr_name), value);
+#endif
+ return PyObject_SetAttr(obj, attr_name, value);
+}
+#endif
+
/* PyErrFetchRestore */
#if CYTHON_FAST_THREAD_STATE
static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) {
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static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) {
int ret;
PyObject *name_attr;
- name_attr = __Pyx_PyObject_GetAttrStr(meth, __pyx_n_s_name);
+ name_attr = __Pyx_PyObject_GetAttrStr(meth, __pyx_n_s_name_2);
if (likely(name_attr)) {
ret = PyObject_RichCompareBool(name_attr, name, Py_EQ);
} else {
diff --git a/src/screening/kappa_test.pyx b/src/screening/gap_test_p_1.pyx
similarity index 85%
rename from src/screening/kappa_test.pyx
rename to src/screening/gap_test_p_1.pyx
index 07f8def3d1b47793d9cd0fc1ba02f225898c2fd3..369afdd87394a0bed898c3c988718783d08aaddd 100644
--- a/src/screening/kappa_test.pyx
+++ b/src/screening/gap_test_p_1.pyx
@@ -20,7 +20,7 @@ from cpython.mem cimport PyMem_Malloc, PyMem_Realloc, PyMem_Free
#(AbstractGapScreening)
-cdef class Kappa_test:
+cdef class GapTestPequalOne:
""" Generalized test
"""
@@ -72,14 +72,13 @@ cdef class Kappa_test:
# (1. + vec_coherence_function) * np.arange(1, n+1, dtype=np.double)
# ).copy()
+ self.name = "Gap test p=1 (cython)"
+
def __dealloc__(self):
PyMem_Free(self.vec_cumsum_gammas) # no-op if self.data is NULL
PyMem_Free(self.vec_kappa_q) # no-op if self.data is NULL
- def get_name(self):
- return "kappa-test cython"
-
@cython.boundscheck(False) # turn off bounds-checking for entire function
@cython.wraparound(False) # turn off negative index wrapping for entire function
@@ -87,7 +86,8 @@ cdef class Kappa_test:
np.ndarray[np.npy_double, ndim=1] Atcabs,
double gap,
double lbd,
- np.ndarray[np.npy_double, ndim=1] vec_gammas,
+ np.ndarray[np.npy_double, ndim=1] vec_gammas,
+ double coeff_dual_scaling = 1.,
double offset_radius=0.,
np.ndarray[long, ndim=1] index=None
):
@@ -107,6 +107,14 @@ cdef class Kappa_test:
vec_gammas : np.ndarray
slope parameters
size [n,]
+ vec_gammas : np.ndarray
+ slope parameters
+ size [n,]
+ coeff_dual_scaling : positif float
+ If coeff_dual_scaling is not feasible, dual scaling factor
+ such taht vecu / coeff_dual_scaling os dual feasible
+ Here for code optimization purposes
+ Default value is 1. (vecu is feasible)
offset_radius : float
additive term added to the redius
default is 0
@@ -127,7 +135,8 @@ cdef class Kappa_test:
cdef int l_min = 0
cdef double bound
- cdef double radius = np.sqrt(2 * gap) + offset_radius
+ cdef double radius = coeff_dual_scaling * np.sqrt(2 * gap) + offset_radius
+ cdef double coeff_lbd = coeff_dual_scaling * lbd
cdef np.ndarray[np.npy_double, ndim=1] sigmas = np.zeros(n+1)
@@ -142,7 +151,7 @@ cdef class Kappa_test:
sigmas[1:] = np.cumsum(Atcabs[index])
for q in range(n-1, -1, -1):
- bound = lbd * self.vec_cumsum_gammas[q] - self.vec_kappa_q[q] * radius - sigmas[q]
+ bound = coeff_lbd * self.vec_cumsum_gammas[q] - self.vec_kappa_q[q] * radius - sigmas[q]
if Atcabs[index[q]] < bound:
l_q = 0
diff --git a/src/screening/singletest.py b/src/screening/gap_test_p_q.py
similarity index 62%
rename from src/screening/singletest.py
rename to src/screening/gap_test_p_q.py
index 7bd5c149945a0c1c503587d31910ddb164295586..6520ba0eed1d3660c07cd6da6ecf4a5ce9b56599 100644
--- a/src/screening/singletest.py
+++ b/src/screening/gap_test_p_q.py
@@ -4,15 +4,15 @@ import numpy as np
from src.screening.ascreening import AbstractGapScreening
-class GapSphereSingleTest(AbstractGapScreening):
+class GapTestPequalQ(AbstractGapScreening):
""" Single test safe sphere screening test for Slope
"""
def __init__(self):
- super(GapSphereSingleTest, self).__init__()
+ super(GapTestPequalQ, self).__init__()
- self.name = "single test"
+ self.name = "Gap test p=q"
- def apply_test(self, Atu_abs, gap, lbd, vec_gammas, offset_radius=0, index=None) -> np.ndarray:
+ def apply_test(self, Atu_abs, gap, lbd, vec_gammas, coeff_dual_scaling=1., offset_radius=0, index=None) -> np.ndarray:
""" GAP Sphere screening test detailed in Cédric's node
Parameters
@@ -27,6 +27,11 @@ class GapSphereSingleTest(AbstractGapScreening):
vec_gammas : np.ndarray
slope parameters
size [n,]
+ coeff_dual_scaling : positif float
+ If coeff_dual_scaling is not feasible, dual scaling factor
+ such taht vecu / coeff_dual_scaling os dual feasible
+ Here for code optimization purposes
+ Default value is 1. (vecu is feasible)
offset_radius : float
additive term added to the redius
index : np.ndarray
@@ -43,4 +48,4 @@ class GapSphereSingleTest(AbstractGapScreening):
"""
radius = np.sqrt(2 * gap)
- return Atu_abs < lbd * vec_gammas[-1] - radius - offset_radius
+ return Atu_abs < coeff_dual_scaling * (lbd * vec_gammas[-1] - radius) - offset_radius
diff --git a/src/solver/parameters.py b/src/solver/parameters.py
index 1fb75215fb23827aca5b90de4119d1d2ef0088a9..7fd921d0e24686f703da303caf8f4511c4ee45a6 100755
--- a/src/solver/parameters.py
+++ b/src/solver/parameters.py
@@ -8,31 +8,53 @@ from src.screening.ascreening import AbstractGapScreening
class EnumLipchitzOptions(enum.Enum):
- EXACT = enum.auto()
- GERSHGORIN = enum.auto()
+ EXACT = enum.auto()
+ GERSHGORIN = enum.auto()
+ BACKTRACKING = enum.auto()
+
+
+class DualScalingOptions(enum.Enum):
+ EXACT = enum.auto()
+ BAO_ET_AL = enum.auto()
class MyList:
- def __getitem__(self, key):
- return float(key)
+ def __getitem__(self, key):
+ return float(key)
+
@dataclass
class SlopeParameters(object):
- max_it: int = 1e3
- gap_stopping: float = 1e-9
- time_stopping: float = 1e2
- accelerated: bool = False
- vecx_init: np.ndarray = None
- verbose: bool = True
+ max_it: int = 1e3
+ gap_stopping: float = 1e-9
+ time_stopping: float = 1e2
+ accelerated: bool = False
+ vecx_init: np.ndarray = None
+ verbose: bool = True
+
+ dual_scaling: DualScalingOptions = DualScalingOptions.EXACT
+
+ eval_gap: bool = True
+
+ lipchitz_constant: float = None
+ lipchitz_update: EnumLipchitzOptions = EnumLipchitzOptions.EXACT
+
+ coherence: float = 1.
+ coherence_function: np.ndarray = MyList()
+
+ screening1: AbstractGapScreening = None
+ screening2: AbstractGapScreening = None
+ screening_it_div: float = 2.
+
+ save_nactive: bool = False
+ save_pfunc: bool = False
+ save_dfunc: bool = False
+
+
+
+# @dataclass
+# class SlopeParameters(AlgParameters):
- lipchitz_constant: float = None
- lipchitz_update: EnumLipchitzOptions = EnumLipchitzOptions.EXACT
- coherence: float = 1.
- coherence_function: np.ndarray = MyList()
- screening1: AbstractGapScreening = None
- screening2: AbstractGapScreening = None
- screening_it_div: float = 2.
- save_nactive = False
diff --git a/src/solver/slope.py b/src/solver/slope.py
index a247786fc6e4495b55a9732bdef8b30fcbee57f5..ada599c2161584414d0ddfe8e0dba7867292db01 100755
--- a/src/solver/slope.py
+++ b/src/solver/slope.py
@@ -3,8 +3,8 @@ import time
import numpy as np
-from src.solver.parameters import SlopeParameters, EnumLipchitzOptions
-from src.solver.prox import prox_owl
+from src.parameters import SlopeParameters, EnumLipchitzOptions, DualScalingOptions
+from src.prox import prox_owl
def primal_func(vecy, Ax, x, lbd, vec_gammas) -> float:
@@ -85,6 +85,7 @@ def slope_gp(vecy, matA, lbd, vecgamma, algParameters=SlopeParameters()):
# Precomputed quantities
Aty = matA.T @ vecy
normy2 = np.linalg.norm(vecy)**2
+ gamma_returned = vecgamma[::-1]
# Coherence
mu = algParameters.coherence
@@ -124,6 +125,8 @@ def slope_gp(vecy, matA, lbd, vecgamma, algParameters=SlopeParameters()):
screening_test_1 = algParameters.screening1
screening_test_2 = algParameters.screening2
+ vec_cumsum_gammas = np.cumsum(vecgamma)
+
is_test_1 = False if screening_test_1 is None else True
is_test_2 = False if screening_test_2 is None else True
@@ -145,10 +148,13 @@ def slope_gp(vecy, matA, lbd, vecgamma, algParameters=SlopeParameters()):
best_costfunc = .5 * normy2
best_vecx = np.copy(vecx_hat)
- best_vecu = np.zeros(m)
best_dualfunc = 0
it = 0
+
+ # Security to prevent error with negative gap
+ gap_stop = max(algParameters.gap_stopping, 5e-16)
+
time_starting = time.time()
ellapsed_time = lambda: time.time() - time_starting
while True:
@@ -160,34 +166,55 @@ def slope_gp(vecy, matA, lbd, vecgamma, algParameters=SlopeParameters()):
vec_res = vecy - Ax
neg_grad = matA[:, ind_active].T @ vec_res
- # Dual scaling
- index_sort_neg_grad = np.argsort(np.abs(neg_grad))[::-1]
- beta_dual = np.abs(neg_grad[index_sort_neg_grad])
- beta_dual = np.cumsum(beta_dual) / np.cumsum(vecgamma[:n_active])
- max_beta_dual = max(np.max(beta_dual) / lbd, 1.)
- vecu_hat = vec_res / max_beta_dual
+ # -- Evaluating primal function
+ # I drop the idea below. it is the "best strategy" only when evaluating the dual function
+ # ytAx = vecy.dot(Ax)
+ # normAx2 = np.linalg.norm(Ax, 2)**2
+ half_norm_res_2 = .5 * np.linalg.norm(vec_res, 2)**2
+ lbd_slope_norm = lbd * gamma_returned.dot(np.sort(np.abs(vecx_hat[ind_active])))
- vec_cost_func.append(primal_func(vecy, Ax, vecx_hat[ind_active], lbd, vecgamma[:n_active]))
- vec_dual_func.append(dual_func(vecy, normy2, vecu_hat))
+ vec_cost_func.append(half_norm_res_2 + lbd_slope_norm)
if vec_cost_func[-1] < best_costfunc:
best_costfunc = vec_cost_func[-1]
best_vecx = np.copy(vecx_hat)
- if vec_dual_func[-1] > best_dualfunc:
- best_dualfunc = vec_dual_func[-1]
- best_vecu = np.copy(vecu_hat)
+ gap = best_costfunc
+
+ if (it % 20 == 0) or algParameters.eval_gap:
+ # -- Evaluating dual function (if needed)
+ # if algParameters.eval_gap:
+ index_sort_neg_grad = np.argsort(np.abs(neg_grad))[::-1]
+ # print(index_sort_neg_grad)
+
+ # Dual scaling
+ if algParameters.dual_scaling == DualScalingOptions.EXACT:
+ beta_dual = np.cumsum(np.abs(neg_grad[index_sort_neg_grad])) \
+ / vec_cumsum_gammas[:n_active]
+ coeff_dual_scaling = max(np.max(beta_dual) / lbd, 1.)
+
+ elif algParameters.dual_scaling == DualScalingOptions.BAO_ET_AL:
+ beta_dual = np.abs(neg_grad[index_sort_neg_grad]) / vecgamma[:n_active]
+ coeff_dual_scaling = max(np.max(beta_dual) / lbd, 1.)
+
+ else:
+ raise NotImplemented
- gap = np.abs(best_costfunc - best_dualfunc)
- # print(f"it {it} gap {gap}")
+ yT_res = vecy.dot(vec_res)
+ d_func_val = (yT_res - half_norm_res_2 / coeff_dual_scaling) / coeff_dual_scaling
+
+ if algParameters.save_dfunc:
+ vec_dual_func.append(d_func_val)
+
+ gap = np.abs(best_costfunc - d_func_val)
# ------------------
# Stopping rules
# ------------------
- if (it >= algParameters.max_it) or (gap <= algParameters.gap_stopping) or (ellapsed_time() > algParameters.time_stopping):
+ if (it >= algParameters.max_it) or (gap <= gap_stop) or (ellapsed_time() > algParameters.time_stopping):
break
@@ -195,16 +222,45 @@ def slope_gp(vecy, matA, lbd, vecgamma, algParameters=SlopeParameters()):
# Screening
# ------------------
- if is_test_1 or is_test_2:
+ if (it % 20 == 0) and (is_test_1 or is_test_2):
+ # -- Evaluating dual function (if needed)
+ # if algParameters.eval_gap:
+ index_sort_neg_grad = np.argsort(np.abs(neg_grad))[::-1]
+ # print(index_sort_neg_grad)
+
+ # Dual scaling
+ if algParameters.dual_scaling == DualScalingOptions.EXACT:
+ beta_dual = np.cumsum(np.abs(neg_grad[index_sort_neg_grad])) \
+ / vec_cumsum_gammas[:n_active]
+ coeff_dual_scaling = max(np.max(beta_dual) / lbd, 1.)
- Atu = neg_grad / max_beta_dual
- gap_test = np.abs(vec_cost_func[-1] - vec_dual_func[-1])
+ elif algParameters.dual_scaling == DualScalingOptions.BAO_ET_AL:
+ beta_dual = np.abs(neg_grad[index_sort_neg_grad]) / vecgamma[:n_active]
+ coeff_dual_scaling = max(np.max(beta_dual) / lbd, 1.)
+
+ else:
+ raise NotImplemented
- # print(np.max(np.abs(Atu)), np.max(np.abs(matA.T @ vecu_hat)), lbd * vecgamma[:n_active])
+ yT_res = vecy.dot(vec_res)
+ d_func_val = (yT_res - half_norm_res_2 / coeff_dual_scaling) / coeff_dual_scaling
+
+ # vec_dual_func.append(dualfunc)
+
+ # we take vec_dual_func[-1] because the corresponding u is used for
+ # the GAP ball
+ # gap = np.abs(best_costfunc - vec_dual_func[-1])
+ gap = np.abs(best_costfunc - d_func_val)
+
+ # Potential improvements
+ # - l218: Atu coulb commented
+ # - l225: Atu coulb replaced by neg_grad and lbd by "coeff_dual_scaling * lbd" (+ radius)
+ # - l242: idem
+ # Atu = neg_grad / coeff_dual_scaling
+ # gap = np.abs(best_costfunc - vec_dual_func[-1])
# 1. Apply test
- if is_test_2 and do_test2(gap, gap_last_test):
- out_test2 = screening_test_2.apply_test(np.abs(Atu), gap_test, lbd, vecgamma[:n_active], index=index_sort_neg_grad)
+ if is_test_2: # and do_test2(gap, gap_last_test):
+ out_test2 = screening_test_2.apply_test(np.abs(neg_grad), gap, lbd, vecgamma[:n_active], coeff_dual_scaling=coeff_dual_scaling, index=index_sort_neg_grad)
if np.any(out_test2):
# 2a. Set entry to 0
@@ -213,15 +269,17 @@ def slope_gp(vecy, matA, lbd, vecgamma, algParameters=SlopeParameters()):
# 2b. Reduce set of active indices
neg_grad = neg_grad[np.bitwise_not(out_test2)]
ind_active = ind_active[np.bitwise_not(out_test2)]
- n_active -= np.sum(out_test2)
+ nb_screen = np.sum(out_test2)
+ n_active -= nb_screen
+
+ gamma_returned = gamma_returned[nb_screen:]
# schedule next test
- gap_last_test = float(gap_test)
- # print("all", n_active)
+ gap_last_test = float(gap)
lip = update_Lip()
elif is_test_1:
- out_test1 = screening_test_1.apply_test(np.abs(Atu), gap_test, lbd, vecgamma[:n_active], index=index_sort_neg_grad)
+ out_test1 = screening_test_1.apply_test(np.abs(neg_grad), gap, lbd, vecgamma[:n_active], coeff_dual_scaling=coeff_dual_scaling, index=index_sort_neg_grad)
if np.any(out_test1):
# 2a. Set entry to 0
@@ -230,9 +288,10 @@ def slope_gp(vecy, matA, lbd, vecgamma, algParameters=SlopeParameters()):
# 2b. Reduce set of active indices
neg_grad = neg_grad[np.bitwise_not(out_test1)]
ind_active = ind_active[np.bitwise_not(out_test1)]
- n_active -= np.sum(out_test1)
- # print("single", n_active)
+ nb_screen = np.sum(out_test1)
+ n_active -= nb_screen
+ gamma_returned = gamma_returned[nb_screen:]
lip = update_Lip()
@@ -270,12 +329,12 @@ def slope_gp(vecy, matA, lbd, vecgamma, algParameters=SlopeParameters()):
time_run = ellapsed_time()
+
return {
"sol": best_vecx,
- "dualsol": best_vecu,
"cost_function": np.array(vec_cost_func),
"dual_function": np.array(vec_dual_func),
- "gap": gap, #Best gap
+ "gap": gap,
"time_run": time_run,
"nb_it": it,
"vec_n_active": np.array(vec_n_active),