Generated by Cython 0.29.30
Yellow lines hint at Python interaction.
Click on a line that starts with a "+
" to see the C code that Cython generated for it.
Raw output: urs_ext.c
+001: #cython: wraparound=False, boundscheck=False, cdivision=True, profile=False, nonecheck=False, overflowcheck=False, cdivision_warnings=False, unraisable_tracebacks=False
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002: import cython
003: from libc.stdlib cimport malloc, free
004: # import both numpy and the Cython declarations for numpy
+005: import numpy as np
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006: cimport numpy as np
007:
008: # declare the interface to the C code
009: cdef extern from "urs.c":
010: float** _read_mux2(int numSrc, char** muxFileNameArray, float* weights, double* params, int* number_of_stations, long* permutation, int verbose)
011:
+012: def read_mux2(int numSrc,\
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013: list filenames,\
014: np.ndarray[double, ndim=1, mode="c"] pyweights not None,\
015: np.ndarray[double, ndim=1, mode="c"] file_params not None,\
016: np.ndarray[long, ndim=1, mode="c"] permutation not None,\
017: int verbose):
018: # Make sure filenames are cast as str().encode(). This will work in both Python2 and Python3 (Ole)
019:
020: cdef char** muxFileNameArray
021: cdef float** cdata
022: cdef float* weights
023: cdef int dimensions[2]
024: cdef int total_number_of_stations
025: cdef int number_of_selected_stations
026: cdef int nt
027: cdef double dt
028: cdef int i, j, start_tstep, finish_tstep, it, time, num_ts
+029: cdef int POFFSET = 5
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030: cdef np.ndarray[double, ndim=2, mode="c"] pydata
031: cdef np.ndarray[long, ndim=1, mode="c"] tmp_perm
032:
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034:
+035: assert len(filenames) > 0, "empty lists not allowed"
#ifndef CYTHON_WITHOUT_ASSERTIONS if (unlikely(!Py_OptimizeFlag)) { if (unlikely(__pyx_v_filenames == Py_None)) { PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); __PYX_ERR(0, 35, __pyx_L1_error) } __pyx_t_11 = PyList_GET_SIZE(__pyx_v_filenames); if (unlikely(__pyx_t_11 == ((Py_ssize_t)-1))) __PYX_ERR(0, 35, __pyx_L1_error) if (unlikely(!((__pyx_t_11 > 0) != 0))) { PyErr_SetObject(PyExc_AssertionError, __pyx_kp_s_empty_lists_not_allowed); __PYX_ERR(0, 35, __pyx_L1_error) } } #endif
036:
+037: assert len(filenames) == pyweights.shape[0], "Must specify one weight for each filename"
#ifndef CYTHON_WITHOUT_ASSERTIONS if (unlikely(!Py_OptimizeFlag)) { if (unlikely(__pyx_v_filenames == Py_None)) { PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); __PYX_ERR(0, 37, __pyx_L1_error) } __pyx_t_11 = PyList_GET_SIZE(__pyx_v_filenames); if (unlikely(__pyx_t_11 == ((Py_ssize_t)-1))) __PYX_ERR(0, 37, __pyx_L1_error) if (unlikely(!((__pyx_t_11 == (__pyx_v_pyweights->dimensions[0])) != 0))) { PyErr_SetObject(PyExc_AssertionError, __pyx_kp_s_Must_specify_one_weight_for_each); __PYX_ERR(0, 37, __pyx_L1_error) } } #endif
038:
+039: muxFileNameArray = <char** > malloc(numSrc * sizeof(char*))
__pyx_v_muxFileNameArray = ((char **)malloc((__pyx_v_numSrc * (sizeof(char *)))));
+040: assert muxFileNameArray != NULL, "ERROR: Memory for muxFileNameArray could not be allocated."
#ifndef CYTHON_WITHOUT_ASSERTIONS if (unlikely(!Py_OptimizeFlag)) { if (unlikely(!((__pyx_v_muxFileNameArray != NULL) != 0))) { PyErr_SetObject(PyExc_AssertionError, __pyx_kp_s_ERROR_Memory_for_muxFileNameArra); __PYX_ERR(0, 40, __pyx_L1_error) } } #endif
041:
+042: for i in xrange(numSrc):
__pyx_t_5 = __pyx_v_numSrc; __pyx_t_12 = __pyx_t_5; for (__pyx_t_13 = 0; __pyx_t_13 < __pyx_t_12; __pyx_t_13+=1) { __pyx_v_i = __pyx_t_13;
043: #assert isinstance(filenames[i], basestring), "filename not a string" # Nor should it be ;-)
044: #print(filenames[i], type(filenames[i]))
+045: muxFileNameArray[i] = filenames[i]
if (unlikely(__pyx_v_filenames == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); __PYX_ERR(0, 45, __pyx_L1_error) } __pyx_t_14 = __Pyx_PyObject_AsWritableString(PyList_GET_ITEM(__pyx_v_filenames, __pyx_v_i)); if (unlikely((!__pyx_t_14) && PyErr_Occurred())) __PYX_ERR(0, 45, __pyx_L1_error) (__pyx_v_muxFileNameArray[__pyx_v_i]) = __pyx_t_14; }
046:
+047: weights = <float* > malloc(numSrc * sizeof(float))
__pyx_v_weights = ((float *)malloc((__pyx_v_numSrc * (sizeof(float)))));
+048: assert weights != NULL, "ERROR: Memory for weights could not be allocated."
#ifndef CYTHON_WITHOUT_ASSERTIONS if (unlikely(!Py_OptimizeFlag)) { if (unlikely(!((__pyx_v_weights != NULL) != 0))) { PyErr_SetObject(PyExc_AssertionError, __pyx_kp_s_ERROR_Memory_for_weights_could_n); __PYX_ERR(0, 48, __pyx_L1_error) } } #endif
049:
+050: for i in xrange(numSrc):
__pyx_t_5 = __pyx_v_numSrc; __pyx_t_12 = __pyx_t_5; for (__pyx_t_13 = 0; __pyx_t_13 < __pyx_t_12; __pyx_t_13+=1) { __pyx_v_i = __pyx_t_13;
+051: weights[i] = pyweights[i]
__pyx_t_15 = __pyx_v_i; (__pyx_v_weights[__pyx_v_i]) = (*__Pyx_BufPtrCContig1d(double *, __pyx_pybuffernd_pyweights.rcbuffer->pybuffer.buf, __pyx_t_15, __pyx_pybuffernd_pyweights.diminfo[0].strides)); }
052:
+053: number_of_selected_stations = permutation.shape[0]
__pyx_v_number_of_selected_stations = (__pyx_v_permutation->dimensions[0]);
054:
+055: if number_of_selected_stations == 0:
__pyx_t_16 = ((__pyx_v_number_of_selected_stations == 0) != 0); if (__pyx_t_16) { /* … */ }
+056: permutation = tmp_perm
{ __Pyx_BufFmt_StackElem __pyx_stack[1]; __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_permutation.rcbuffer->pybuffer); __pyx_t_5 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_permutation.rcbuffer->pybuffer, (PyObject*)((PyArrayObject *)__pyx_v_tmp_perm), &__Pyx_TypeInfo_long, PyBUF_FORMAT| PyBUF_C_CONTIGUOUS, 1, 0, __pyx_stack); if (unlikely(__pyx_t_5 < 0)) { PyErr_Fetch(&__pyx_t_10, &__pyx_t_9, &__pyx_t_8); if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_permutation.rcbuffer->pybuffer, (PyObject*)__pyx_v_permutation, &__Pyx_TypeInfo_long, PyBUF_FORMAT| PyBUF_C_CONTIGUOUS, 1, 0, __pyx_stack) == -1)) { Py_XDECREF(__pyx_t_10); Py_XDECREF(__pyx_t_9); Py_XDECREF(__pyx_t_8); __Pyx_RaiseBufferFallbackError(); } else { PyErr_Restore(__pyx_t_10, __pyx_t_9, __pyx_t_8); } __pyx_t_10 = __pyx_t_9 = __pyx_t_8 = 0; } __pyx_pybuffernd_permutation.diminfo[0].strides = __pyx_pybuffernd_permutation.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_permutation.diminfo[0].shape = __pyx_pybuffernd_permutation.rcbuffer->pybuffer.shape[0]; if (unlikely(__pyx_t_5 < 0)) __PYX_ERR(0, 56, __pyx_L1_error) } __Pyx_INCREF(((PyObject *)__pyx_v_tmp_perm)); __Pyx_DECREF_SET(__pyx_v_permutation, ((PyArrayObject *)__pyx_v_tmp_perm));
057:
+058: cdata = _read_mux2(numSrc,\
__pyx_v_cdata = _read_mux2(__pyx_v_numSrc, __pyx_v_muxFileNameArray, __pyx_v_weights, (&(*__Pyx_BufPtrCContig1d(double *, __pyx_pybuffernd_file_params.rcbuffer->pybuffer.buf, __pyx_t_15, __pyx_pybuffernd_file_params.diminfo[0].strides))), (&__pyx_v_number_of_selected_stations), (&(*__Pyx_BufPtrCContig1d(long *, __pyx_pybuffernd_permutation.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_permutation.diminfo[0].strides))), __pyx_v_verbose);
059: muxFileNameArray,\
060: weights,\
+061: &file_params[0],\
__pyx_t_15 = 0;
062: &number_of_selected_stations,\
+063: &permutation[0],\
__pyx_t_17 = 0;
064: verbose)
065:
+066: assert cdata != NULL, "No STS_DATA returned"
#ifndef CYTHON_WITHOUT_ASSERTIONS if (unlikely(!Py_OptimizeFlag)) { if (unlikely(!((__pyx_v_cdata != NULL) != 0))) { PyErr_SetObject(PyExc_AssertionError, __pyx_kp_s_No_STS_DATA_returned); __PYX_ERR(0, 66, __pyx_L1_error) } } #endif
067:
+068: total_number_of_stations = int(file_params[0])
__pyx_t_17 = 0; __pyx_v_total_number_of_stations = ((int)(*__Pyx_BufPtrCContig1d(double *, __pyx_pybuffernd_file_params.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_file_params.diminfo[0].strides)));
+069: dt = file_params[1]
__pyx_t_17 = 1; __pyx_v_dt = (*__Pyx_BufPtrCContig1d(double *, __pyx_pybuffernd_file_params.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_file_params.diminfo[0].strides));
+070: nt = int(file_params[2])
__pyx_t_17 = 2; __pyx_v_nt = ((int)(*__Pyx_BufPtrCContig1d(double *, __pyx_pybuffernd_file_params.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_file_params.diminfo[0].strides)));
071:
072: # Find min and max start times of all gauges
+073: start_tstep = nt + 1
__pyx_v_start_tstep = (__pyx_v_nt + 1);
+074: finish_tstep = -1
__pyx_v_finish_tstep = -1;
+075: for i in xrange(number_of_selected_stations):
__pyx_t_5 = __pyx_v_number_of_selected_stations; __pyx_t_12 = __pyx_t_5; for (__pyx_t_13 = 0; __pyx_t_13 < __pyx_t_12; __pyx_t_13+=1) { __pyx_v_i = __pyx_t_13;
+076: if int(cdata[i][nt + 3]) < start_tstep:
__pyx_t_1 = __Pyx_PyInt_FromDouble(((__pyx_v_cdata[__pyx_v_i])[(__pyx_v_nt + 3)])); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 76, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_start_tstep); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 76, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __pyx_t_6 = PyObject_RichCompare(__pyx_t_1, __pyx_t_3, Py_LT); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 76, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_16 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_16 < 0)) __PYX_ERR(0, 76, __pyx_L1_error) __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; if (__pyx_t_16) { /* … */ }
+077: start_tstep = int(cdata[i][nt + 3])
__pyx_v_start_tstep = ((int)((__pyx_v_cdata[__pyx_v_i])[(__pyx_v_nt + 3)]));
+078: if int(cdata[i][nt + 4]) > finish_tstep:
__pyx_t_6 = __Pyx_PyInt_FromDouble(((__pyx_v_cdata[__pyx_v_i])[(__pyx_v_nt + 4)])); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 78, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_6); __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_finish_tstep); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 78, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __pyx_t_1 = PyObject_RichCompare(__pyx_t_6, __pyx_t_3, Py_GT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 78, __pyx_L1_error) __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_16 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_16 < 0)) __PYX_ERR(0, 78, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_16) { /* … */ } }
+079: finish_tstep = int(cdata[i][nt + 4])
__pyx_v_finish_tstep = ((int)((__pyx_v_cdata[__pyx_v_i])[(__pyx_v_nt + 4)]));
080:
+081: if start_tstep > nt or finish_tstep < 0:
__pyx_t_18 = ((__pyx_v_start_tstep > __pyx_v_nt) != 0); if (!__pyx_t_18) { } else { __pyx_t_16 = __pyx_t_18; goto __pyx_L13_bool_binop_done; } __pyx_t_18 = ((__pyx_v_finish_tstep < 0) != 0); __pyx_t_16 = __pyx_t_18; __pyx_L13_bool_binop_done:; if (__pyx_t_16) { /* … */ }
+082: print "ERROR: Gauge data has incorrect start and finish times:"
if (__Pyx_PrintOne(0, __pyx_kp_s_ERROR_Gauge_data_has_incorrect_s) < 0) __PYX_ERR(0, 82, __pyx_L1_error)
+083: print " start_tstep = %d, max_number_of_steps = %d" % (start_tstep, nt)
__pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_start_tstep); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 83, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_nt); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 83, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 83, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_6); __Pyx_GIVEREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_3); __pyx_t_1 = 0; __pyx_t_3 = 0; __pyx_t_3 = __Pyx_PyString_Format(__pyx_kp_s_start_tstep_d_max_number_of_ste, __pyx_t_6); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 83, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; if (__Pyx_PrintOne(0, __pyx_t_3) < 0) __PYX_ERR(0, 83, __pyx_L1_error) __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+084: print " finish_tstep = %d, min_number_of_steps = %d" % (finish_tstep, 0)
__pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_finish_tstep); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 84, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 84, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_6); __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_3); __Pyx_INCREF(__pyx_int_0); __Pyx_GIVEREF(__pyx_int_0); PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_int_0); __pyx_t_3 = 0; __pyx_t_3 = __Pyx_PyString_Format(__pyx_kp_s_finish_tstep_d_min_number_of_st, __pyx_t_6); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 84, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; if (__Pyx_PrintOne(0, __pyx_t_3) < 0) __PYX_ERR(0, 84, __pyx_L1_error) __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
085:
+086: assert start_tstep <= nt and finish_tstep >= 0, "Incorrect start and finish times"
#ifndef CYTHON_WITHOUT_ASSERTIONS if (unlikely(!Py_OptimizeFlag)) { __pyx_t_18 = ((__pyx_v_start_tstep <= __pyx_v_nt) != 0); if (__pyx_t_18) { } else { __pyx_t_16 = __pyx_t_18; goto __pyx_L15_bool_binop_done; } __pyx_t_18 = ((__pyx_v_finish_tstep >= 0) != 0); __pyx_t_16 = __pyx_t_18; __pyx_L15_bool_binop_done:; if (unlikely(!__pyx_t_16)) { PyErr_SetObject(PyExc_AssertionError, __pyx_kp_s_Incorrect_start_and_finish_times); __PYX_ERR(0, 86, __pyx_L1_error) } } #endif
087:
+088: free(weights)
free(__pyx_v_weights);
+089: free(muxFileNameArray)
free(__pyx_v_muxFileNameArray);
090:
+091: for i in xrange(number_of_selected_stations):
__pyx_t_5 = __pyx_v_number_of_selected_stations; __pyx_t_12 = __pyx_t_5; for (__pyx_t_13 = 0; __pyx_t_13 < __pyx_t_12; __pyx_t_13+=1) { __pyx_v_i = __pyx_t_13;
+092: free(cdata[i])
free((__pyx_v_cdata[__pyx_v_i])); }
+093: free(cdata)
free(__pyx_v_cdata);
094:
+095: if start_tstep >= finish_tstep:
__pyx_t_16 = ((__pyx_v_start_tstep >= __pyx_v_finish_tstep) != 0); if (__pyx_t_16) { /* … */ }
+096: assert start_tstep < finish_tstep, "ERROR: Gauge data has non-positive length"
#ifndef CYTHON_WITHOUT_ASSERTIONS if (unlikely(!Py_OptimizeFlag)) { if (unlikely(!((__pyx_v_start_tstep < __pyx_v_finish_tstep) != 0))) { PyErr_SetObject(PyExc_AssertionError, __pyx_kp_s_ERROR_Gauge_data_has_non_positiv); __PYX_ERR(0, 96, __pyx_L1_error) } } #endif
+097: free(weights)
free(__pyx_v_weights);
+098: free(muxFileNameArray)
free(__pyx_v_muxFileNameArray);
+099: for i in xrange(number_of_selected_stations):
__pyx_t_5 = __pyx_v_number_of_selected_stations; __pyx_t_12 = __pyx_t_5; for (__pyx_t_13 = 0; __pyx_t_13 < __pyx_t_12; __pyx_t_13+=1) { __pyx_v_i = __pyx_t_13;
+100: free(cdata[i])
free((__pyx_v_cdata[__pyx_v_i])); }
+101: free(cdata)
free(__pyx_v_cdata);
102:
+103: num_ts = finish_tstep - start_tstep + 1
__pyx_v_num_ts = ((__pyx_v_finish_tstep - __pyx_v_start_tstep) + 1);
+104: dimensions[0] = number_of_selected_stations
(__pyx_v_dimensions[0]) = __pyx_v_number_of_selected_stations;
+105: dimensions[1] = num_ts + POFFSET
(__pyx_v_dimensions[1]) = (__pyx_v_num_ts + __pyx_v_POFFSET);
106:
107: # Each gauge begins and ends recording at different times. When a gauge is
108: # not recording but at least one other gauge is.
109: # Pad the non recording gauge array with zeros.
+110: pydata = np.zeros((dimensions[0],dimensions[1]),dtype=float)
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128:
129: