diff --git a/MANIFEST.in b/MANIFEST.in index 5a8747a..6f73d38 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,3 +1,2 @@ recursive-include */Resources *.* -include compass/compass/extensions/tsne_utils.pyx diff --git a/compass/_version.py b/compass/_version.py index 513931e..47c2b02 100644 --- a/compass/_version.py +++ b/compass/_version.py @@ -1,4 +1,4 @@ # Store the version here to be imported by both the # setup.py file and the package's init module -__version__ = "0.9.9.6.2" +__version__ = "0.9.9.6.3" diff --git a/compass/compass/extensions/__init__.py b/compass/compass/extensions/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/compass/compass/extensions/tsne_utils.c b/compass/compass/extensions/tsne_utils.c deleted file mode 100644 index bd08279..0000000 --- a/compass/compass/extensions/tsne_utils.c +++ /dev/null @@ -1,8451 +0,0 @@ -/* Generated by Cython 0.24.1 */ - -/* BEGIN: Cython Metadata -{ - "distutils": { - "depends": [ - "/data/yosef2/users/david.detomaso/programs/anaconda3/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h", - "/data/yosef2/users/david.detomaso/programs/anaconda3/lib/python3.5/site-packages/numpy/core/include/numpy/npy_math.h", - "/data/yosef2/users/david.detomaso/programs/anaconda3/lib/python3.5/site-packages/numpy/core/include/numpy/ufuncobject.h" - ], - "include_dirs": [ - "/data/yosef2/users/david.detomaso/programs/anaconda3/lib/python3.5/site-packages/numpy/core/include" - ] - }, - "module_name": "compass.compass.extensions.tsne_utils" -} -END: Cython Metadata */ - -#define PY_SSIZE_T_CLEAN -#include "Python.h" -#ifndef Py_PYTHON_H - #error Python headers needed to compile C extensions, please install development version of Python. -#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) - #error Cython requires Python 2.6+ or Python 3.2+. -#else -#define CYTHON_ABI "0_24_1" -#include -#ifndef offsetof - #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) -#endif -#if !defined(WIN32) && !defined(MS_WINDOWS) - #ifndef __stdcall - #define __stdcall - #endif - #ifndef __cdecl - #define __cdecl - #endif - #ifndef __fastcall - #define __fastcall - #endif -#endif -#ifndef DL_IMPORT - #define DL_IMPORT(t) t -#endif -#ifndef DL_EXPORT - #define DL_EXPORT(t) t -#endif -#ifndef PY_LONG_LONG - #define PY_LONG_LONG LONG_LONG -#endif -#ifndef Py_HUGE_VAL - #define Py_HUGE_VAL HUGE_VAL -#endif -#ifdef PYPY_VERSION - #define CYTHON_COMPILING_IN_PYPY 1 - #define CYTHON_COMPILING_IN_CPYTHON 0 -#else - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_CPYTHON 1 -#endif -#if !defined(CYTHON_USE_PYLONG_INTERNALS) && CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x02070000 - #define CYTHON_USE_PYLONG_INTERNALS 1 -#endif -#if CYTHON_USE_PYLONG_INTERNALS - #include "longintrepr.h" - #undef SHIFT - #undef BASE - #undef MASK -#endif -#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) - #define Py_OptimizeFlag 0 -#endif -#define __PYX_BUILD_PY_SSIZE_T "n" -#define CYTHON_FORMAT_SSIZE_T "z" -#if PY_MAJOR_VERSION < 3 - #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) - #define __Pyx_DefaultClassType PyClass_Type -#else - #define __Pyx_BUILTIN_MODULE_NAME "builtins" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) - #define __Pyx_DefaultClassType PyType_Type -#endif -#ifndef Py_TPFLAGS_CHECKTYPES - #define Py_TPFLAGS_CHECKTYPES 0 -#endif -#ifndef Py_TPFLAGS_HAVE_INDEX - #define Py_TPFLAGS_HAVE_INDEX 0 -#endif -#ifndef Py_TPFLAGS_HAVE_NEWBUFFER - #define Py_TPFLAGS_HAVE_NEWBUFFER 0 -#endif -#ifndef Py_TPFLAGS_HAVE_FINALIZE - #define Py_TPFLAGS_HAVE_FINALIZE 0 -#endif -#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) - #define CYTHON_PEP393_ENABLED 1 - #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ - 0 : _PyUnicode_Ready((PyObject *)(op))) - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) - #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) - #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) - #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? 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- 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 CYTHON_INLINE PyObject * -__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) -{ - const char *ts = *tsp; - int i = 0, number; - int ndim = ctx->head->field->type->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; - 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_IsLittleEndian()) { - PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '>': - case '!': - if (__Pyx_IsLittleEndian()) { - 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; - } - 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->enc_count += ctx->new_count; - ctx->new_count = 1; - got_Z = 0; - ++ts; - break; - } - 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; - } - } - } -} -static CYTHON_INLINE 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 CYTHON_INLINE int __Pyx_GetBufferAndValidate( - Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, - int nd, int cast, __Pyx_BufFmt_StackElem* stack) -{ - if (obj == Py_None || obj == NULL) { - __Pyx_ZeroBuffer(buf); - return 0; - } - buf->buf = NULL; - if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail; - if (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 ((unsigned)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_ZeroBuffer(buf); - return -1; -} -static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { - if (info->buf == NULL) return; - if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; - __Pyx_ReleaseBuffer(info); -} - -/* GetModuleGlobalName */ - static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) { - PyObject *result; -#if CYTHON_COMPILING_IN_CPYTHON - result = PyDict_GetItem(__pyx_d, name); - if (likely(result)) { - Py_INCREF(result); - } else { -#else - result = PyObject_GetItem(__pyx_d, name); - if (!result) { - PyErr_Clear(); -#endif - result = __Pyx_GetBuiltinName(name); - } - return result; -} - -/* PyObjectCall */ - #if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { - PyObject *result; - ternaryfunc call = func->ob_type->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 - -/* 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(PyObject_TypeCheck(obj, type))) - return 1; - PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", - Py_TYPE(obj)->tp_name, type->tp_name); - return 0; -} - -/* None */ - static CYTHON_INLINE long __Pyx_mod_long(long a, long b) { - long r = a % b; - r += ((r != 0) & ((r ^ b) < 0)) * b; - return r; -} - -/* 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) { -#ifdef __Pyx_CyFunction_USED - if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) { -#else - if (likely(PyCFunction_Check(func))) { -#endif - if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { - return __Pyx_PyObject_CallMethO(func, arg); - } - } - 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 - -/* PyErrFetchRestore */ - #if CYTHON_COMPILING_IN_CPYTHON -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 - -/* RaiseArgTupleInvalid */ - static void __Pyx_RaiseArgtupleInvalid( - const char* func_name, - int exact, - Py_ssize_t num_min, - Py_ssize_t num_max, - Py_ssize_t num_found) -{ - Py_ssize_t num_expected; - const char *more_or_less; - if (num_found < num_min) { - num_expected = num_min; - more_or_less = "at least"; - } else { - num_expected = num_max; - more_or_less = "at most"; - } - if (exact) { - more_or_less = "exactly"; - } - PyErr_Format(PyExc_TypeError, - "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", - func_name, more_or_less, num_expected, - (num_expected == 1) ? "" : "s", num_found); -} - -/* RaiseDoubleKeywords */ - static void __Pyx_RaiseDoubleKeywordsError( - const char* func_name, - PyObject* kw_name) -{ - PyErr_Format(PyExc_TypeError, - #if PY_MAJOR_VERSION >= 3 - "%s() got multiple values for keyword argument '%U'", func_name, kw_name); - #else - "%s() got multiple values for keyword argument '%s'", func_name, - PyString_AsString(kw_name)); - #endif -} - -/* ParseKeywords */ - static int __Pyx_ParseOptionalKeywords( - PyObject *kwds, - PyObject **argnames[], - PyObject *kwds2, - PyObject *values[], - Py_ssize_t num_pos_args, - const char* function_name) -{ - PyObject *key = 0, *value = 0; - Py_ssize_t pos = 0; - PyObject*** name; - PyObject*** first_kw_arg = argnames + num_pos_args; - while (PyDict_Next(kwds, &pos, &key, &value)) { - name = first_kw_arg; - while (*name && (**name != key)) name++; - if (*name) { - values[name-argnames] = value; - continue; - } - name = first_kw_arg; - #if PY_MAJOR_VERSION < 3 - if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { - while (*name) { - if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) - && _PyString_Eq(**name, key)) { - values[name-argnames] = value; - break; - } - name++; - } - if (*name) continue; - else { - PyObject*** argname = argnames; - while (argname != first_kw_arg) { - if ((**argname == key) || ( - (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) - && _PyString_Eq(**argname, key))) { - goto arg_passed_twice; - } - argname++; - } - } - } else - #endif - if (likely(PyUnicode_Check(key))) { - while (*name) { - int cmp = (**name == key) ? 0 : - #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : - #endif - PyUnicode_Compare(**name, key); - if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; - if (cmp == 0) { - values[name-argnames] = value; - break; - } - name++; - } - if (*name) continue; - else { - PyObject*** argname = argnames; - while (argname != first_kw_arg) { - int cmp = (**argname == key) ? 0 : - #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : - #endif - PyUnicode_Compare(**argname, key); - if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; - if (cmp == 0) goto arg_passed_twice; - argname++; - } - } - } else - goto invalid_keyword_type; - if (kwds2) { - if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; - } else { - goto invalid_keyword; - } - } - return 0; -arg_passed_twice: - __Pyx_RaiseDoubleKeywordsError(function_name, key); - goto bad; -invalid_keyword_type: - PyErr_Format(PyExc_TypeError, - "%.200s() keywords must be strings", function_name); - goto bad; -invalid_keyword: - PyErr_Format(PyExc_TypeError, - #if PY_MAJOR_VERSION < 3 - "%.200s() got an unexpected keyword argument '%.200s'", - function_name, PyString_AsString(key)); - #else - "%s() got an unexpected keyword argument '%U'", - function_name, key); - #endif -bad: - return -1; -} - -/* ArgTypeTest */ - static void __Pyx_RaiseArgumentTypeInvalid(const char* name, PyObject *obj, PyTypeObject *type) { - PyErr_Format(PyExc_TypeError, - "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)", - name, type->tp_name, Py_TYPE(obj)->tp_name); -} -static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, - const char *name, int exact) -{ - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - if (none_allowed && obj == Py_None) return 1; - else if (exact) { - if (likely(Py_TYPE(obj) == type)) return 1; - #if PY_MAJOR_VERSION == 2 - else if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; - #endif - } - else { - if (likely(PyObject_TypeCheck(obj, type))) return 1; - } - __Pyx_RaiseArgumentTypeInvalid(name, obj, type); - return 0; -} - -/* 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 PY_VERSION_HEX >= 0x03030000 - if (cause) { -#else - if (cause && cause != Py_None) { -#endif - 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 = PyThreadState_GET(); - 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 - -/* RaiseTooManyValuesToUnpack */ - static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { - PyErr_Format(PyExc_ValueError, - "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); -} - -/* RaiseNeedMoreValuesToUnpack */ - static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { - PyErr_Format(PyExc_ValueError, - "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", - index, (index == 1) ? "" : "s"); -} - -/* RaiseNoneIterError */ - static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { - PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); -} - -/* 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_VERSION_HEX < 0x03030000 - 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 (strchr(__Pyx_MODULE_NAME, '.')) { - #if PY_VERSION_HEX < 0x03030000 - PyObject *py_level = PyInt_FromLong(1); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, 1); - #endif - if (!module) { - if (!PyErr_ExceptionMatches(PyExc_ImportError)) - goto bad; - PyErr_Clear(); - } - } - level = 0; - } - #endif - if (!module) { - #if PY_VERSION_HEX < 0x03030000 - PyObject *py_level = PyInt_FromLong(level); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, level); - #endif - } - } -bad: - #if PY_VERSION_HEX < 0x03030000 - Py_XDECREF(py_import); - #endif - Py_XDECREF(empty_list); - Py_XDECREF(empty_dict); - return module; -} - -/* 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; - 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( - PyThreadState_GET(), /*PyThreadState *tstate,*/ - py_code, /*PyCodeObject *code,*/ - __pyx_d, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (!py_frame) goto bad; - py_frame->f_lineno = 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); - if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__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 (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } - Py_DECREF(obj); - view->obj = NULL; -} -#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;\ - } - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { - const long neg_one = (long) -1, const_zero = (long) 0; - 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); - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); - } - } else { - if (sizeof(long) <= sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), - little, !is_unsigned); - } -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { - const int neg_one = (int) -1, const_zero = (int) 0; - 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); - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); - } - } else { - if (sizeof(int) <= sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(int), - little, !is_unsigned); - } -} - -/* Print */ - #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION < 3 -static PyObject *__Pyx_GetStdout(void) { - PyObject *f = PySys_GetObject((char *)"stdout"); - if (!f) { - PyErr_SetString(PyExc_RuntimeError, "lost sys.stdout"); - } - return f; -} -static int __Pyx_Print(PyObject* f, PyObject *arg_tuple, int newline) { - int i; - if (!f) { - if (!(f = __Pyx_GetStdout())) - return -1; - } - Py_INCREF(f); - for (i=0; i < PyTuple_GET_SIZE(arg_tuple); i++) { - PyObject* v; - if (PyFile_SoftSpace(f, 1)) { - if (PyFile_WriteString(" ", f) < 0) - goto error; - } - v = PyTuple_GET_ITEM(arg_tuple, i); - if (PyFile_WriteObject(v, f, Py_PRINT_RAW) < 0) - goto error; - if (PyString_Check(v)) { - char *s = PyString_AsString(v); - Py_ssize_t len = PyString_Size(v); - if (len > 0) { - switch (s[len-1]) { - case ' ': break; - case '\f': case '\r': case '\n': case '\t': case '\v': - PyFile_SoftSpace(f, 0); - break; - default: break; - } - } - } - } - if (newline) { - if (PyFile_WriteString("\n", f) < 0) - goto error; - PyFile_SoftSpace(f, 0); - } - Py_DECREF(f); - return 0; -error: - Py_DECREF(f); - return -1; -} -#else -static int __Pyx_Print(PyObject* stream, PyObject *arg_tuple, int newline) { - PyObject* kwargs = 0; - PyObject* result = 0; - PyObject* end_string; - if (unlikely(!__pyx_print)) { - __pyx_print = PyObject_GetAttr(__pyx_b, __pyx_n_s_print); - if (!__pyx_print) - return -1; - } - if (stream) { - kwargs = PyDict_New(); - if (unlikely(!kwargs)) - return -1; - if (unlikely(PyDict_SetItem(kwargs, __pyx_n_s_file, stream) < 0)) - goto bad; - if (!newline) { - end_string = PyUnicode_FromStringAndSize(" ", 1); - if (unlikely(!end_string)) - goto bad; - if (PyDict_SetItem(kwargs, __pyx_n_s_end, end_string) < 0) { - Py_DECREF(end_string); - goto bad; - } - Py_DECREF(end_string); - } - } else if (!newline) { - if (unlikely(!__pyx_print_kwargs)) { - __pyx_print_kwargs = PyDict_New(); - if (unlikely(!__pyx_print_kwargs)) - return -1; - end_string = PyUnicode_FromStringAndSize(" ", 1); - if (unlikely(!end_string)) - return -1; - if (PyDict_SetItem(__pyx_print_kwargs, __pyx_n_s_end, end_string) < 0) { - Py_DECREF(end_string); - return -1; - } - Py_DECREF(end_string); - } - kwargs = __pyx_print_kwargs; - } - result = PyObject_Call(__pyx_print, arg_tuple, kwargs); - if (unlikely(kwargs) && (kwargs != __pyx_print_kwargs)) - Py_DECREF(kwargs); - if (!result) - return -1; - Py_DECREF(result); - return 0; -bad: - if (kwargs != __pyx_print_kwargs) - Py_XDECREF(kwargs); - return -1; -} -#endif - -/* None */ - #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 - -/* None */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eqf(__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_sumf(__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_difff(__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_prodf(__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; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - float denom = b.real * b.real + b.imag * b.imag; - z.real = (a.real * b.real + a.imag * b.imag) / denom; - z.imag = (a.imag * b.real - a.real * b.imag) / denom; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__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_zerof(__pyx_t_float_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__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_absf(__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_powf(__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: - z = __Pyx_c_prodf(a, a); - return __Pyx_c_prodf(a, a); - case 3: - z = __Pyx_c_prodf(a, a); - return __Pyx_c_prodf(z, a); - case 4: - z = __Pyx_c_prodf(a, a); - return __Pyx_c_prodf(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } - r = a.real; - theta = 0; - } else { - r = __Pyx_c_absf(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 - -/* None */ - #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 - -/* None */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq(__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(__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(__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(__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; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - double denom = b.real * b.real + b.imag * b.imag; - z.real = (a.real * b.real + a.imag * b.imag) / denom; - z.imag = (a.imag * b.real - a.real * b.imag) / denom; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__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(__pyx_t_double_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__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(__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(__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: - z = __Pyx_c_prod(a, a); - return __Pyx_c_prod(a, a); - case 3: - z = __Pyx_c_prod(a, a); - return __Pyx_c_prod(z, a); - case 4: - z = __Pyx_c_prod(a, a); - return __Pyx_c_prod(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } - r = a.real; - theta = 0; - } else { - r = __Pyx_c_abs(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_enum__NPY_TYPES(enum NPY_TYPES value) { - const enum NPY_TYPES neg_one = (enum NPY_TYPES) -1, const_zero = (enum NPY_TYPES) 0; - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(enum NPY_TYPES) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); - } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); - } - } else { - if (sizeof(enum NPY_TYPES) <= sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(enum NPY_TYPES) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(enum NPY_TYPES), - little, !is_unsigned); - } -} - -/* CIntFromPy */ - static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { - const int neg_one = (int) -1, const_zero = (int) 0; - 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)) - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) - } - } 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)) - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) - } - } - { -#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; -} - -/* CIntFromPy */ - static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { - const long neg_one = (long) -1, const_zero = (long) 0; - 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)) - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) - } - } 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) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (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) - 1 > 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 (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) - } - } - { -#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 - 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 (long) -1; - } - } else { - 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; -} - -/* PrintOne */ - #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION < 3 -static int __Pyx_PrintOne(PyObject* f, PyObject *o) { - if (!f) { - if (!(f = __Pyx_GetStdout())) - return -1; - } - Py_INCREF(f); - if (PyFile_SoftSpace(f, 0)) { - if (PyFile_WriteString(" ", f) < 0) - goto error; - } - if (PyFile_WriteObject(o, f, Py_PRINT_RAW) < 0) - goto error; - if (PyFile_WriteString("\n", f) < 0) - goto error; - Py_DECREF(f); - return 0; -error: - Py_DECREF(f); - return -1; - /* the line below is just to avoid C compiler - * warnings about unused functions */ - return __Pyx_Print(f, NULL, 0); -} -#else -static int __Pyx_PrintOne(PyObject* stream, PyObject *o) { - int res; - PyObject* arg_tuple = PyTuple_Pack(1, o); - if (unlikely(!arg_tuple)) - return -1; - res = __Pyx_Print(stream, arg_tuple, 1); - Py_DECREF(arg_tuple); - return res; -} -#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; -} - -/* ModuleImport */ - #ifndef __PYX_HAVE_RT_ImportModule -#define __PYX_HAVE_RT_ImportModule -static PyObject *__Pyx_ImportModule(const char *name) { - PyObject *py_name = 0; - PyObject *py_module = 0; - py_name = __Pyx_PyIdentifier_FromString(name); - if (!py_name) - goto bad; - py_module = PyImport_Import(py_name); - Py_DECREF(py_name); - return py_module; -bad: - Py_XDECREF(py_name); - return 0; -} -#endif - -/* TypeImport */ - #ifndef __PYX_HAVE_RT_ImportType -#define __PYX_HAVE_RT_ImportType -static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, - size_t size, int strict) -{ - PyObject *py_module = 0; - PyObject *result = 0; - PyObject *py_name = 0; - char warning[200]; - Py_ssize_t basicsize; -#ifdef Py_LIMITED_API - PyObject *py_basicsize; -#endif - py_module = __Pyx_ImportModule(module_name); - if (!py_module) - goto bad; - py_name = __Pyx_PyIdentifier_FromString(class_name); - if (!py_name) - goto bad; - result = PyObject_GetAttr(py_module, py_name); - Py_DECREF(py_name); - py_name = 0; - Py_DECREF(py_module); - py_module = 0; - 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 (!strict && (size_t)basicsize > size) { - PyOS_snprintf(warning, sizeof(warning), - "%s.%s size changed, may indicate binary incompatibility. Expected %zd, got %zd", - module_name, class_name, basicsize, size); - if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; - } - else if ((size_t)basicsize != size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s has the wrong size, try recompiling. Expected %zd, got %zd", - module_name, class_name, basicsize, size); - goto bad; - } - return (PyTypeObject *)result; -bad: - Py_XDECREF(py_module); - Py_XDECREF(result); - return NULL; -} -#endif - -/* 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; - ++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 char* __Pyx_PyObject_AsString(PyObject* o) { - Py_ssize_t ignore; - return __Pyx_PyObject_AsStringAndSize(o, &ignore); -} -static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { -#if CYTHON_COMPILING_IN_CPYTHON && (__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)) { -#if PY_VERSION_HEX < 0x03030000 - 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 - if (__Pyx_PyUnicode_READY(o) == -1) return NULL; -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - if (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 - } 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 PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) { - PyNumberMethods *m; - const char *name = NULL; - PyObject *res = NULL; -#if PY_MAJOR_VERSION < 3 - if (PyInt_Check(x) || PyLong_Check(x)) -#else - if (PyLong_Check(x)) -#endif - return __Pyx_NewRef(x); - m = Py_TYPE(x)->tp_as_number; -#if PY_MAJOR_VERSION < 3 - if (m && m->nb_int) { - name = "int"; - res = PyNumber_Int(x); - } - else if (m && m->nb_long) { - name = "long"; - res = PyNumber_Long(x); - } -#else - if (m && m->nb_int) { - name = "int"; - res = PyNumber_Long(x); - } -#endif - if (res) { -#if PY_MAJOR_VERSION < 3 - if (!PyInt_Check(res) && !PyLong_Check(res)) { -#else - if (!PyLong_Check(res)) { -#endif - PyErr_Format(PyExc_TypeError, - "__%.4s__ returned non-%.4s (type %.200s)", - name, name, Py_TYPE(res)->tp_name); - Py_DECREF(res); - return NULL; - } - } - 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(x); - } -#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_PyInt_FromSize_t(size_t ival) { - return PyInt_FromSize_t(ival); -} - - -#endif /* Py_PYTHON_H */ diff --git a/compass/compass/extensions/tsne_utils.pyx b/compass/compass/extensions/tsne_utils.pyx deleted file mode 100644 index ea626cd..0000000 --- a/compass/compass/extensions/tsne_utils.pyx +++ /dev/null @@ -1,299 +0,0 @@ -""" -New BSD License - -Copyright (c) 20072017 The scikit-learn developers. -All rights reserved. - - -Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are met: - - a. Redistributions of source code must retain the above copyright notice, - this list of conditions and the following disclaimer. - b. Redistributions in binary form must reproduce the above copyright - notice, this list of conditions and the following disclaimer in the - documentation and/or other materials provided with the distribution. - c. Neither the name of the Scikit-learn Developers nor the names of - its contributors may be used to endorse or promote products - derived from this software without specific prior written - permission. - - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE -ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR -ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL -DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR -SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER -CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT -LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY -OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH -DAMAGE. -""" -from libc cimport math -cimport cython -import numpy as np -cimport numpy as np -from libc.stdio cimport printf -cdef extern from "numpy/npy_math.h": - float NPY_INFINITY - - -cdef float EPSILON_DBL = 1e-8 -cdef float PERPLEXITY_TOLERANCE = 1e-5 - -@cython.boundscheck(False) -cpdef np.ndarray[np.float32_t, ndim=2] binary_search_perplexity( - np.ndarray[np.float32_t, ndim=2] affinities, - np.ndarray[np.int64_t, ndim=2] neighbors, - float desired_perplexity, - int verbose): - """Binary search for sigmas of conditional Gaussians. - - This approximation reduces the computational complexity from O(N^2) to - O(uN). See the exact method '_binary_search_perplexity' for more details. - - Parameters - ---------- - affinities : array-like, shape (n_samples, n_samples) - Distances between training samples. - - neighbors : array-like, shape (n_samples, K) or None - Each row contains the indices to the K nearest neigbors. If this - array is None, then the perplexity is estimated over all data - not just the nearest neighbors. - - desired_perplexity : float - Desired perplexity (2^entropy) of the conditional Gaussians. - - verbose : int - Verbosity level. - - Returns - ------- - P : array, shape (n_samples, n_samples) - Probabilities of conditional Gaussian distributions p_i|j. - """ - # Maximum number of binary search steps - cdef long n_steps = 100 - - cdef long n_samples = affinities.shape[0] - # This array is later used as a 32bit array. It has multiple intermediate - # floating point additions that benefit from the extra precision - cdef np.ndarray[np.float64_t, ndim=2] P = np.zeros((n_samples, n_samples), - dtype=np.float64) - # Precisions of conditional Gaussian distrubutions - cdef float beta - cdef float beta_min - cdef float beta_max - cdef float beta_sum = 0.0 - # Now we go to log scale - cdef float desired_entropy = math.log(desired_perplexity) - cdef float entropy_diff - - cdef float entropy - cdef float sum_Pi - cdef float sum_disti_Pi - cdef long i, j, k, l = 0 - cdef long K = n_samples - cdef int using_neighbors = neighbors is not None - - if using_neighbors: - K = neighbors.shape[1] - - for i in range(n_samples): - beta_min = -NPY_INFINITY - beta_max = NPY_INFINITY - beta = 1.0 - - # Binary search of precision for i-th conditional distribution - for l in range(n_steps): - # Compute current entropy and corresponding probabilities - # computed just over the nearest neighbors or over all data - # if we're not using neighbors - if using_neighbors: - for k in range(K): - j = neighbors[i, k] - P[i, j] = math.exp(-affinities[i, j] * beta) - else: - for j in range(K): - P[i, j] = math.exp(-affinities[i, j] * beta) - P[i, i] = 0.0 - sum_Pi = 0.0 - if using_neighbors: - for k in range(K): - j = neighbors[i, k] - sum_Pi += P[i, j] - else: - for j in range(K): - sum_Pi += P[i, j] - if sum_Pi == 0.0: - sum_Pi = EPSILON_DBL - sum_disti_Pi = 0.0 - if using_neighbors: - for k in range(K): - j = neighbors[i, k] - P[i, j] /= sum_Pi - sum_disti_Pi += affinities[i, j] * P[i, j] - else: - for j in range(K): - P[i, j] /= sum_Pi - sum_disti_Pi += affinities[i, j] * P[i, j] - entropy = math.log(sum_Pi) + beta * sum_disti_Pi - entropy_diff = entropy - desired_entropy - - if math.fabs(entropy_diff) <= PERPLEXITY_TOLERANCE: - break - - if entropy_diff > 0.0: - beta_min = beta - if beta_max == NPY_INFINITY: - beta *= 2.0 - else: - beta = (beta + beta_max) / 2.0 - else: - beta_max = beta - if beta_min == -NPY_INFINITY: - beta /= 2.0 - else: - beta = (beta + beta_min) / 2.0 - - beta_sum += beta - - if verbose and ((i + 1) % 1000 == 0 or i + 1 == n_samples): - print("[t-SNE] Computed conditional probabilities for sample " - "%d / %d" % (i + 1, n_samples)) - - if verbose: - print("[t-SNE] Mean sigma: %f" - % np.mean(math.sqrt(n_samples / beta_sum))) - return P - - -@cython.boundscheck(False) -cpdef np.ndarray[np.float32_t, ndim=1] binary_search_perplexity_single( - np.ndarray[np.float32_t, ndim=1] affinities, - np.ndarray[np.int64_t, ndim=1] neighbors, - float desired_perplexity, - int verbose, int sample): - """Binary search for sigmas of conditional Gaussians. - - This approximation reduces the computational complexity from O(N^2) to - O(uN). See the exact method '_binary_search_perplexity' for more details. - - This version only computes the p-values for a single sample - - Parameters - ---------- - affinities : array-like, shape (n_samples, n_samples) - Distances between training samples. - - neighbors : array-like, shape (n_samples, K) or None - Each row contains the indices to the K nearest neigbors. If this - array is None, then the perplexity is estimated over all data - not just the nearest neighbors. - - desired_perplexity : float - Desired perplexity (2^entropy) of the conditional Gaussians. - - verbose : int - Verbosity level. - - Returns - ------- - P : array, shape (n_samples, n_samples) - Probabilities of conditional Gaussian distributions p_i|j. - """ - # Maximum number of binary search steps - cdef long n_steps = 100 - - cdef long n_samples = affinities.shape[0] - # This array is later used as a 32bit array. It has multiple intermediate - # floating point additions that benefit from the extra precision - cdef np.ndarray[np.float64_t, ndim=1] P = np.zeros(n_samples, dtype=np.float64) - # Precisions of conditional Gaussian distrubutions - cdef float beta - cdef float beta_min - cdef float beta_max - # Now we go to log scale - cdef float desired_entropy = math.log(desired_perplexity) - cdef float entropy_diff - - cdef float entropy - cdef float sum_Pi - cdef float sum_disti_Pi - cdef long i, j, k, l = 0 - cdef long K = n_samples - cdef int using_neighbors = neighbors is not None - - if using_neighbors: - K = neighbors.shape[0] - - i = 0 - cdef long sample_i = sample - - beta_min = -NPY_INFINITY - beta_max = NPY_INFINITY - beta = 1.0 - - # Binary search of precision for i-th conditional distribution - for l in range(n_steps): - # Compute current entropy and corresponding probabilities - # computed just over the nearest neighbors or over all data - # if we're not using neighbors - if using_neighbors: - for k in range(K): - j = neighbors[k] - P[j] = math.exp(-affinities[j] * beta) - else: - for j in range(K): - P[j] = math.exp(-affinities[j] * beta) - - P[sample_i] = 0.0 - sum_Pi = 0.0 - - if using_neighbors: - for k in range(K): - j = neighbors[k] - sum_Pi += P[j] - else: - for j in range(K): - sum_Pi += P[j] - if sum_Pi == 0.0: - sum_Pi = EPSILON_DBL - sum_disti_Pi = 0.0 - - if using_neighbors: - for k in range(K): - j = neighbors[k] - P[j] /= sum_Pi - sum_disti_Pi += affinities[j] * P[j] - else: - for j in range(K): - P[j] /= sum_Pi - sum_disti_Pi += affinities[j] * P[j] - - entropy = math.log(sum_Pi) + beta * sum_disti_Pi - entropy_diff = entropy - desired_entropy - - if math.fabs(entropy_diff) <= PERPLEXITY_TOLERANCE: - break - - if entropy_diff > 0.0: - beta_min = beta - if beta_max == NPY_INFINITY: - beta *= 2.0 - else: - beta = (beta + beta_max) / 2.0 - else: - beta_max = beta - if beta_min == -NPY_INFINITY: - beta /= 2.0 - else: - beta = (beta + beta_min) / 2.0 - - if verbose: - print("[t-SNE] Sigma: %f" % math.sqrt(1 / beta)) - - return P diff --git a/compass/compass/penalties.py b/compass/compass/penalties.py index e837832..3a21910 100644 --- a/compass/compass/penalties.py +++ b/compass/compass/penalties.py @@ -1,12 +1,12 @@ import numpy as np import pandas as pd import logging -from .extensions import tsne_utils from .. import utils from .. import models from ..globals import EXCHANGE_LIMIT, PCA_SEED from sklearn.neighbors import NearestNeighbors from sklearn.decomposition import PCA +from sklearn.manifold._utils import _binary_search_perplexity from scipy import sparse @@ -265,11 +265,10 @@ def sample_weights_tsne_symmetric(data, perplexity, symmetric): aff = aff.astype('float32') # Run the tsne perplexity procedure - pvals = tsne_utils.binary_search_perplexity( - affinities=aff, - neighbors=None, - desired_perplexity=perplexity, - verbose=0 + pvals = _binary_search_perplexity( + aff, + perplexity, + 0 ) # Symmetrize the pvals diff --git a/setup.py b/setup.py index 805ce3e..72f88ab 100644 --- a/setup.py +++ b/setup.py @@ -1,7 +1,5 @@ import os from setuptools import setup, find_packages -from setuptools.extension import Extension -import numpy.distutils # Parse the version string __version__ = "" @@ -9,34 +7,10 @@ version_file = os.path.join(this_directory, "compass", "_version.py") exec(open(version_file).read()) # Loads version into __version__ -# Extensions -try: - from Cython.Build import cythonize - use_cython = True -except ImportError: - use_cython = False - -if use_cython: - extensions = [ - Extension( - "compass.compass.extensions.tsne_utils", - ["compass/compass/extensions/tsne_utils.pyx"], - include_dirs=numpy.distutils.misc_util.get_numpy_include_dirs()) - ] - extensions = cythonize(extensions) -else: - extensions = [ - Extension( - "compass.compass.extensions.tsne_utils", - ["compass/compass/extensions/tsne_utils.c"], - include_dirs=numpy.distutils.misc_util.get_numpy_include_dirs()) - ] - setup( name="compass-sc", version=__version__, packages=find_packages(), - ext_modules=extensions, include_package_data=True, entry_points={'console_scripts':