From cf2d92e151f816e6ddcfc4b64cbda1f8f7bde9df Mon Sep 17 00:00:00 2001 From: Rémi Flamary Date: Fri, 28 Oct 2016 08:53:16 +0200 Subject: complete doc emd --- ot/lp/emd.cpp | 126 +++++++++++++++++++++++++++++----------------------------- 1 file changed, 63 insertions(+), 63 deletions(-) (limited to 'ot/lp/emd.cpp') diff --git a/ot/lp/emd.cpp b/ot/lp/emd.cpp index 2343af6..26d243f 100644 --- a/ot/lp/emd.cpp +++ b/ot/lp/emd.cpp @@ -6,11 +6,11 @@ "depends": [ "/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h", "/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ufuncobject.h", - "ot/emd/EMD.h" + "ot/lp/EMD.h" ], "include_dirs": [ "/usr/lib/python2.7/dist-packages/numpy/core/include", - "/home/rflamary/PYTHON/POT/ot/emd" + "/home/rflamary/PYTHON/POT/ot/lp" ], "language": "c++" } @@ -260,8 +260,8 @@ static CYTHON_INLINE float __PYX_NAN() { #endif #endif -#define __PYX_HAVE__ot__emd__emd -#define __PYX_HAVE_API__ot__emd__emd +#define __PYX_HAVE__ot__lp__emd +#define __PYX_HAVE_API__ot__lp__emd #include "string.h" #include "stdio.h" #include "stdlib.h" @@ -497,7 +497,7 @@ static const char *__pyx_filename; static const char *__pyx_f[] = { - "ot/emd/emd.pyx", + "ot/lp/emd.pyx", "__init__.pxd", "type.pxd", }; @@ -1129,12 +1129,12 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, cha /* Module declarations from 'cython' */ -/* Module declarations from 'ot.emd.emd' */ +/* Module declarations from 'ot.lp.emd' */ static __Pyx_TypeInfo __Pyx_TypeInfo_double = { "double", NULL, sizeof(double), { 0 }, 0, 'R', 0, 0 }; -#define __Pyx_MODULE_NAME "ot.emd.emd" -int __pyx_module_is_main_ot__emd__emd = 0; +#define __Pyx_MODULE_NAME "ot.lp.emd" +int __pyx_module_is_main_ot__lp__emd = 0; -/* Implementation of 'ot.emd.emd' */ +/* Implementation of 'ot.lp.emd' */ static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_RuntimeError; @@ -1161,21 +1161,21 @@ static char __pyx_k_Zg[] = "Zg"; static char __pyx_k_n1[] = "n1"; static char __pyx_k_n2[] = "n2"; static char __pyx_k_np[] = "np"; -static char __pyx_k_emd[] = "emd"; static char __pyx_k_cost[] = "cost"; static char __pyx_k_main[] = "__main__"; static char __pyx_k_ones[] = "ones"; static char __pyx_k_test[] = "__test__"; +static char __pyx_k_emd_c[] = "emd_c"; static char __pyx_k_numpy[] = "numpy"; static char __pyx_k_range[] = "range"; static char __pyx_k_zeros[] = "zeros"; static char __pyx_k_import[] = "__import__"; +static char __pyx_k_ot_lp_emd[] = "ot.lp.emd"; static char __pyx_k_ValueError[] = "ValueError"; -static char __pyx_k_ot_emd_emd[] = "ot.emd.emd"; static char __pyx_k_RuntimeError[] = "RuntimeError"; static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; static char __pyx_k_Created_on_Thu_Sep_11_08_42_08[] = "\nCreated on Thu Sep 11 08:42:08 2014\n\n@author: rflamary\n"; -static char __pyx_k_home_rflamary_PYTHON_POT_ot_emd[] = "/home/rflamary/PYTHON/POT/ot/emd/emd.pyx"; +static char __pyx_k_home_rflamary_PYTHON_POT_ot_lp[] = "/home/rflamary/PYTHON/POT/ot/lp/emd.pyx"; static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; static char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; static char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported"; @@ -1191,8 +1191,8 @@ static PyObject *__pyx_n_s_ValueError; static PyObject *__pyx_n_s_a; static PyObject *__pyx_n_s_b; static PyObject *__pyx_n_s_cost; -static PyObject *__pyx_n_s_emd; -static PyObject *__pyx_kp_s_home_rflamary_PYTHON_POT_ot_emd; +static PyObject *__pyx_n_s_emd_c; +static PyObject *__pyx_kp_s_home_rflamary_PYTHON_POT_ot_lp; static PyObject *__pyx_n_s_import; static PyObject *__pyx_n_s_main; static PyObject *__pyx_n_s_n1; @@ -1202,12 +1202,12 @@ static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou; static PyObject *__pyx_n_s_np; static PyObject *__pyx_n_s_numpy; static PyObject *__pyx_n_s_ones; -static PyObject *__pyx_n_s_ot_emd_emd; +static PyObject *__pyx_n_s_ot_lp_emd; static PyObject *__pyx_n_s_range; static PyObject *__pyx_n_s_test; static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; static PyObject *__pyx_n_s_zeros; -static PyObject *__pyx_pf_2ot_3emd_3emd_emd(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_a, PyArrayObject *__pyx_v_b, PyArrayObject *__pyx_v_M); /* proto */ +static PyObject *__pyx_pf_2ot_2lp_3emd_emd_c(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_a, PyArrayObject *__pyx_v_b, PyArrayObject *__pyx_v_M); /* proto */ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ static PyObject *__pyx_tuple_; @@ -1219,19 +1219,19 @@ static PyObject *__pyx_tuple__6; static PyObject *__pyx_tuple__7; static PyObject *__pyx_codeobj__8; -/* "ot/emd/emd.pyx":21 +/* "ot/lp/emd.pyx":21 * @cython.boundscheck(False) * @cython.wraparound(False) - * def emd( np.ndarray[double, ndim=1, mode="c"] a,np.ndarray[double, ndim=1, mode="c"] b,np.ndarray[double, ndim=2, mode="c"] M): # <<<<<<<<<<<<<< + * def emd_c( np.ndarray[double, ndim=1, mode="c"] a,np.ndarray[double, ndim=1, mode="c"] b,np.ndarray[double, ndim=2, mode="c"] M): # <<<<<<<<<<<<<< * """ * Solves the Earth Movers distance problem and returns the optimal transport matrix */ /* Python wrapper */ -static PyObject *__pyx_pw_2ot_3emd_3emd_1emd(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_2ot_3emd_3emd_emd[] = "\n Solves the Earth Movers distance problem and returns the optimal transport matrix\n \n gamm=emd(a,b,M)\n \n .. math::\n \\gamma = arg\\min_\\gamma <\\gamma,M>_F \n \n s.t. \\gamma 1 = a\n \n \\gamma^T 1= b \n \n \\gamma\\geq 0\n where :\n \n - M is the metric cost matrix\n - a and b are the sample weights\n \n Parameters\n ----------\n a : (ns,) ndarray\n samples in the source domain (uniform waigth if empty)\n b : (nt,) ndarray\n samples in the target domain (uniform waigth if empty)\n M : (ns,nt) ndarray\n loss matrix \n \n \n Returns\n -------\n gamma: (ns x nt) ndarray\n Optimal transportation matrix for the given parameters\n \n "; -static PyMethodDef __pyx_mdef_2ot_3emd_3emd_1emd = {"emd", (PyCFunction)__pyx_pw_2ot_3emd_3emd_1emd, METH_VARARGS|METH_KEYWORDS, __pyx_doc_2ot_3emd_3emd_emd}; -static PyObject *__pyx_pw_2ot_3emd_3emd_1emd(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_2ot_2lp_3emd_1emd_c(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_2ot_2lp_3emd_emd_c[] = "\n Solves the Earth Movers distance problem and returns the optimal transport matrix\n \n gamm=emd(a,b,M)\n \n .. math::\n \\gamma = arg\\min_\\gamma <\\gamma,M>_F \n \n s.t. \\gamma 1 = a\n \n \\gamma^T 1= b \n \n \\gamma\\geq 0\n where :\n \n - M is the metric cost matrix\n - a and b are the sample weights\n \n Parameters\n ----------\n a : (ns,) ndarray\n source histogram \n b : (nt,) ndarray\n target histogram\n M : (ns,nt) ndarray\n loss matrix \n \n \n Returns\n -------\n gamma: (ns x nt) ndarray\n Optimal transportation matrix for the given parameters\n \n "; +static PyMethodDef __pyx_mdef_2ot_2lp_3emd_1emd_c = {"emd_c", (PyCFunction)__pyx_pw_2ot_2lp_3emd_1emd_c, METH_VARARGS|METH_KEYWORDS, __pyx_doc_2ot_2lp_3emd_emd_c}; +static PyObject *__pyx_pw_2ot_2lp_3emd_1emd_c(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyArrayObject *__pyx_v_a = 0; PyArrayObject *__pyx_v_b = 0; PyArrayObject *__pyx_v_M = 0; @@ -1240,7 +1240,7 @@ static PyObject *__pyx_pw_2ot_3emd_3emd_1emd(PyObject *__pyx_self, PyObject *__p int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("emd (wrapper)", 0); + __Pyx_RefNannySetupContext("emd_c (wrapper)", 0); { static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_a,&__pyx_n_s_b,&__pyx_n_s_M,0}; PyObject* values[3] = {0,0,0}; @@ -1262,16 +1262,16 @@ static PyObject *__pyx_pw_2ot_3emd_3emd_1emd(PyObject *__pyx_self, PyObject *__p case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_b)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("emd", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("emd_c", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_M)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("emd", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("emd_c", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "emd") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "emd_c") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 3) { goto __pyx_L5_argtuple_error; @@ -1286,16 +1286,16 @@ static PyObject *__pyx_pw_2ot_3emd_3emd_1emd(PyObject *__pyx_self, PyObject *__p } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("emd", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("emd_c", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("ot.emd.emd.emd", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("ot.lp.emd.emd_c", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_a), __pyx_ptype_5numpy_ndarray, 1, "a", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_b), __pyx_ptype_5numpy_ndarray, 1, "b", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_M), __pyx_ptype_5numpy_ndarray, 1, "M", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_2ot_3emd_3emd_emd(__pyx_self, __pyx_v_a, __pyx_v_b, __pyx_v_M); + __pyx_r = __pyx_pf_2ot_2lp_3emd_emd_c(__pyx_self, __pyx_v_a, __pyx_v_b, __pyx_v_M); /* function exit code */ goto __pyx_L0; @@ -1306,7 +1306,7 @@ static PyObject *__pyx_pw_2ot_3emd_3emd_1emd(PyObject *__pyx_self, PyObject *__p return __pyx_r; } -static PyObject *__pyx_pf_2ot_3emd_3emd_emd(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_a, PyArrayObject *__pyx_v_b, PyArrayObject *__pyx_v_M) { +static PyObject *__pyx_pf_2ot_2lp_3emd_emd_c(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_a, PyArrayObject *__pyx_v_b, PyArrayObject *__pyx_v_M) { int __pyx_v_n1; int __pyx_v_n2; float __pyx_v_cost; @@ -1338,7 +1338,7 @@ static PyObject *__pyx_pf_2ot_3emd_3emd_emd(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; - __Pyx_RefNannySetupContext("emd", 0); + __Pyx_RefNannySetupContext("emd_c", 0); __Pyx_INCREF((PyObject *)__pyx_v_a); __Pyx_INCREF((PyObject *)__pyx_v_b); __pyx_pybuffer_G.pybuffer.buf = NULL; @@ -1373,7 +1373,7 @@ static PyObject *__pyx_pf_2ot_3emd_3emd_emd(CYTHON_UNUSED PyObject *__pyx_self, } __pyx_pybuffernd_M.diminfo[0].strides = __pyx_pybuffernd_M.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_M.diminfo[0].shape = __pyx_pybuffernd_M.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_M.diminfo[1].strides = __pyx_pybuffernd_M.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_M.diminfo[1].shape = __pyx_pybuffernd_M.rcbuffer->pybuffer.shape[1]; - /* "ot/emd/emd.pyx":56 + /* "ot/lp/emd.pyx":56 * * """ * cdef int n1= M.shape[0] # <<<<<<<<<<<<<< @@ -1382,7 +1382,7 @@ static PyObject *__pyx_pf_2ot_3emd_3emd_emd(CYTHON_UNUSED PyObject *__pyx_self, */ __pyx_v_n1 = (__pyx_v_M->dimensions[0]); - /* "ot/emd/emd.pyx":57 + /* "ot/lp/emd.pyx":57 * """ * cdef int n1= M.shape[0] * cdef int n2= M.shape[1] # <<<<<<<<<<<<<< @@ -1391,7 +1391,7 @@ static PyObject *__pyx_pf_2ot_3emd_3emd_emd(CYTHON_UNUSED PyObject *__pyx_self, */ __pyx_v_n2 = (__pyx_v_M->dimensions[1]); - /* "ot/emd/emd.pyx":59 + /* "ot/lp/emd.pyx":59 * cdef int n2= M.shape[1] * * cdef float cost=0 # <<<<<<<<<<<<<< @@ -1400,7 +1400,7 @@ static PyObject *__pyx_pf_2ot_3emd_3emd_emd(CYTHON_UNUSED PyObject *__pyx_self, */ __pyx_v_cost = 0.0; - /* "ot/emd/emd.pyx":60 + /* "ot/lp/emd.pyx":60 * * cdef float cost=0 * cdef np.ndarray[double, ndim=2, mode="c"] G=np.zeros([n1, n2]) # <<<<<<<<<<<<<< @@ -1464,7 +1464,7 @@ static PyObject *__pyx_pf_2ot_3emd_3emd_emd(CYTHON_UNUSED PyObject *__pyx_self, __pyx_v_G = ((PyArrayObject *)__pyx_t_1); __pyx_t_1 = 0; - /* "ot/emd/emd.pyx":62 + /* "ot/lp/emd.pyx":62 * cdef np.ndarray[double, ndim=2, mode="c"] G=np.zeros([n1, n2]) * * if not len(a): # <<<<<<<<<<<<<< @@ -1475,7 +1475,7 @@ static PyObject *__pyx_pf_2ot_3emd_3emd_emd(CYTHON_UNUSED PyObject *__pyx_self, __pyx_t_8 = ((!(__pyx_t_7 != 0)) != 0); if (__pyx_t_8) { - /* "ot/emd/emd.pyx":63 + /* "ot/lp/emd.pyx":63 * * if not len(a): * a=np.ones((n1,))/n1 # <<<<<<<<<<<<<< @@ -1548,7 +1548,7 @@ static PyObject *__pyx_pf_2ot_3emd_3emd_emd(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_DECREF_SET(__pyx_v_a, ((PyArrayObject *)__pyx_t_4)); __pyx_t_4 = 0; - /* "ot/emd/emd.pyx":62 + /* "ot/lp/emd.pyx":62 * cdef np.ndarray[double, ndim=2, mode="c"] G=np.zeros([n1, n2]) * * if not len(a): # <<<<<<<<<<<<<< @@ -1557,7 +1557,7 @@ static PyObject *__pyx_pf_2ot_3emd_3emd_emd(CYTHON_UNUSED PyObject *__pyx_self, */ } - /* "ot/emd/emd.pyx":65 + /* "ot/lp/emd.pyx":65 * a=np.ones((n1,))/n1 * * if not len(b): # <<<<<<<<<<<<<< @@ -1568,7 +1568,7 @@ static PyObject *__pyx_pf_2ot_3emd_3emd_emd(CYTHON_UNUSED PyObject *__pyx_self, __pyx_t_8 = ((!(__pyx_t_7 != 0)) != 0); if (__pyx_t_8) { - /* "ot/emd/emd.pyx":66 + /* "ot/lp/emd.pyx":66 * * if not len(b): * b=np.ones((n2,))/n2 # <<<<<<<<<<<<<< @@ -1641,7 +1641,7 @@ static PyObject *__pyx_pf_2ot_3emd_3emd_emd(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_DECREF_SET(__pyx_v_b, ((PyArrayObject *)__pyx_t_3)); __pyx_t_3 = 0; - /* "ot/emd/emd.pyx":65 + /* "ot/lp/emd.pyx":65 * a=np.ones((n1,))/n1 * * if not len(b): # <<<<<<<<<<<<<< @@ -1650,7 +1650,7 @@ static PyObject *__pyx_pf_2ot_3emd_3emd_emd(CYTHON_UNUSED PyObject *__pyx_self, */ } - /* "ot/emd/emd.pyx":69 + /* "ot/lp/emd.pyx":69 * * # calling the function * EMD_wrap(n1,n2, a.data, b.data, M.data, G.data, &cost) # <<<<<<<<<<<<<< @@ -1659,7 +1659,7 @@ static PyObject *__pyx_pf_2ot_3emd_3emd_emd(CYTHON_UNUSED PyObject *__pyx_self, */ EMD_wrap(__pyx_v_n1, __pyx_v_n2, ((double *)__pyx_v_a->data), ((double *)__pyx_v_b->data), ((double *)__pyx_v_M->data), ((double *)__pyx_v_G->data), ((double *)(&__pyx_v_cost))); - /* "ot/emd/emd.pyx":71 + /* "ot/lp/emd.pyx":71 * EMD_wrap(n1,n2, a.data, b.data, M.data, G.data, &cost) * * return G # <<<<<<<<<<<<<< @@ -1669,10 +1669,10 @@ static PyObject *__pyx_pf_2ot_3emd_3emd_emd(CYTHON_UNUSED PyObject *__pyx_self, __pyx_r = ((PyObject *)__pyx_v_G); goto __pyx_L0; - /* "ot/emd/emd.pyx":21 + /* "ot/lp/emd.pyx":21 * @cython.boundscheck(False) * @cython.wraparound(False) - * def emd( np.ndarray[double, ndim=1, mode="c"] a,np.ndarray[double, ndim=1, mode="c"] b,np.ndarray[double, ndim=2, mode="c"] M): # <<<<<<<<<<<<<< + * def emd_c( np.ndarray[double, ndim=1, mode="c"] a,np.ndarray[double, ndim=1, mode="c"] b,np.ndarray[double, ndim=2, mode="c"] M): # <<<<<<<<<<<<<< * """ * Solves the Earth Movers distance problem and returns the optimal transport matrix */ @@ -1691,7 +1691,7 @@ static PyObject *__pyx_pf_2ot_3emd_3emd_emd(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_a.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_b.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} - __Pyx_AddTraceback("ot.emd.emd.emd", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("ot.lp.emd.emd_c", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; goto __pyx_L2; __pyx_L0:; @@ -3884,8 +3884,8 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_a, __pyx_k_a, sizeof(__pyx_k_a), 0, 0, 1, 1}, {&__pyx_n_s_b, __pyx_k_b, sizeof(__pyx_k_b), 0, 0, 1, 1}, {&__pyx_n_s_cost, __pyx_k_cost, sizeof(__pyx_k_cost), 0, 0, 1, 1}, - {&__pyx_n_s_emd, __pyx_k_emd, sizeof(__pyx_k_emd), 0, 0, 1, 1}, - {&__pyx_kp_s_home_rflamary_PYTHON_POT_ot_emd, __pyx_k_home_rflamary_PYTHON_POT_ot_emd, sizeof(__pyx_k_home_rflamary_PYTHON_POT_ot_emd), 0, 0, 1, 0}, + {&__pyx_n_s_emd_c, __pyx_k_emd_c, sizeof(__pyx_k_emd_c), 0, 0, 1, 1}, + {&__pyx_kp_s_home_rflamary_PYTHON_POT_ot_lp, __pyx_k_home_rflamary_PYTHON_POT_ot_lp, sizeof(__pyx_k_home_rflamary_PYTHON_POT_ot_lp), 0, 0, 1, 0}, {&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1}, {&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1}, {&__pyx_n_s_n1, __pyx_k_n1, sizeof(__pyx_k_n1), 0, 0, 1, 1}, @@ -3895,7 +3895,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__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_n_s_ones, __pyx_k_ones, sizeof(__pyx_k_ones), 0, 0, 1, 1}, - {&__pyx_n_s_ot_emd_emd, __pyx_k_ot_emd_emd, sizeof(__pyx_k_ot_emd_emd), 0, 0, 1, 1}, + {&__pyx_n_s_ot_lp_emd, __pyx_k_ot_lp_emd, sizeof(__pyx_k_ot_lp_emd), 0, 0, 1, 1}, {&__pyx_n_s_range, __pyx_k_range, sizeof(__pyx_k_range), 0, 0, 1, 1}, {&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1}, {&__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_k_unknown_dtype_code_in_numpy_pxd, sizeof(__pyx_k_unknown_dtype_code_in_numpy_pxd), 0, 1, 0, 0}, @@ -3981,17 +3981,17 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__6); __Pyx_GIVEREF(__pyx_tuple__6); - /* "ot/emd/emd.pyx":21 + /* "ot/lp/emd.pyx":21 * @cython.boundscheck(False) * @cython.wraparound(False) - * def emd( np.ndarray[double, ndim=1, mode="c"] a,np.ndarray[double, ndim=1, mode="c"] b,np.ndarray[double, ndim=2, mode="c"] M): # <<<<<<<<<<<<<< + * def emd_c( np.ndarray[double, ndim=1, mode="c"] a,np.ndarray[double, ndim=1, mode="c"] b,np.ndarray[double, ndim=2, mode="c"] M): # <<<<<<<<<<<<<< * """ * Solves the Earth Movers distance problem and returns the optimal transport matrix */ __pyx_tuple__7 = PyTuple_Pack(7, __pyx_n_s_a, __pyx_n_s_b, __pyx_n_s_M, __pyx_n_s_n1, __pyx_n_s_n2, __pyx_n_s_cost, __pyx_n_s_G); if (unlikely(!__pyx_tuple__7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__7); __Pyx_GIVEREF(__pyx_tuple__7); - __pyx_codeobj__8 = (PyObject*)__Pyx_PyCode_New(3, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__7, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_rflamary_PYTHON_POT_ot_emd, __pyx_n_s_emd, 21, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_codeobj__8 = (PyObject*)__Pyx_PyCode_New(3, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__7, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_rflamary_PYTHON_POT_ot_lp, __pyx_n_s_emd_c, 21, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_RefNannyFinishContext(); return 0; __pyx_L1_error:; @@ -4073,14 +4073,14 @@ PyMODINIT_FUNC PyInit_emd(void) #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_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif - if (__pyx_module_is_main_ot__emd__emd) { + if (__pyx_module_is_main_ot__lp__emd) { if (PyObject_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if PY_MAJOR_VERSION >= 3 { PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (!PyDict_GetItemString(modules, "ot.emd.emd")) { - if (unlikely(PyDict_SetItemString(modules, "ot.emd.emd", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!PyDict_GetItemString(modules, "ot.lp.emd")) { + if (unlikely(PyDict_SetItemString(modules, "ot.lp.emd", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } } #endif @@ -4112,7 +4112,7 @@ PyMODINIT_FUNC PyInit_emd(void) if (__Pyx_patch_abc() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif - /* "ot/emd/emd.pyx":7 + /* "ot/lp/emd.pyx":7 * @author: rflamary * """ * import numpy as np # <<<<<<<<<<<<<< @@ -4124,19 +4124,19 @@ PyMODINIT_FUNC PyInit_emd(void) if (PyDict_SetItem(__pyx_d, __pyx_n_s_np, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "ot/emd/emd.pyx":21 + /* "ot/lp/emd.pyx":21 * @cython.boundscheck(False) * @cython.wraparound(False) - * def emd( np.ndarray[double, ndim=1, mode="c"] a,np.ndarray[double, ndim=1, mode="c"] b,np.ndarray[double, ndim=2, mode="c"] M): # <<<<<<<<<<<<<< + * def emd_c( np.ndarray[double, ndim=1, mode="c"] a,np.ndarray[double, ndim=1, mode="c"] b,np.ndarray[double, ndim=2, mode="c"] M): # <<<<<<<<<<<<<< * """ * Solves the Earth Movers distance problem and returns the optimal transport matrix */ - __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_2ot_3emd_3emd_1emd, NULL, __pyx_n_s_ot_emd_emd); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_2ot_2lp_3emd_1emd_c, NULL, __pyx_n_s_ot_lp_emd); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (PyDict_SetItem(__pyx_d, __pyx_n_s_emd, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_d, __pyx_n_s_emd_c, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "ot/emd/emd.pyx":1 + /* "ot/lp/emd.pyx":1 * # -*- coding: utf-8 -*- # <<<<<<<<<<<<<< * """ * Created on Thu Sep 11 08:42:08 2014 @@ -4161,11 +4161,11 @@ PyMODINIT_FUNC PyInit_emd(void) __Pyx_XDECREF(__pyx_t_1); if (__pyx_m) { if (__pyx_d) { - __Pyx_AddTraceback("init ot.emd.emd", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("init ot.lp.emd", __pyx_clineno, __pyx_lineno, __pyx_filename); } Py_DECREF(__pyx_m); __pyx_m = 0; } else if (!PyErr_Occurred()) { - PyErr_SetString(PyExc_ImportError, "init ot.emd.emd"); + PyErr_SetString(PyExc_ImportError, "init ot.lp.emd"); 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