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Raw output: urs_ext.c

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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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 034: 
+035:   assert len(filenames) > 0, "empty lists not allowed"
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    if (unlikely(__pyx_v_filenames == Py_None)) {
      PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
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    }
  }
  #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()");
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    __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)
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      PyErr_SetObject(PyExc_AssertionError, __pyx_kp_s_Must_specify_one_weight_for_each);
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  }
  #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."
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  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):
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    __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)
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    __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."
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    if (unlikely(!((__pyx_v_weights != NULL) != 0))) {
      PyErr_SetObject(PyExc_AssertionError, __pyx_kp_s_ERROR_Memory_for_weights_could_n);
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    }
  }
  #endif
 049: 
+050:   for i in xrange(numSrc):
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  __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);
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    __Pyx_DECREF_SET(__pyx_v_permutation, ((PyArrayObject *)__pyx_v_tmp_perm));
 057: 
+058:   cdata = _read_mux2(numSrc,\
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 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)
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  #endif
 067: 
+068:   total_number_of_stations = int(file_params[0])
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+069:   dt = file_params[1]
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+070:   nt = int(file_params[2])
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 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)
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    __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;
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    __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)
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    __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);
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    __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);
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    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)
  __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_np); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 110, __pyx_L1_error)
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