Generated by Cython 0.20.1 on Tue Apr 29 19:54:33 2014
Raw output: complete.c
1: # cython: profile=True
__pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
2: import time
__pyx_t_1 = __Pyx_Import(__pyx_n_s_time, 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyDict_SetItem(__pyx_d, __pyx_n_s_time, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
3: import json
__pyx_t_1 = __Pyx_Import(__pyx_n_s_json, 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyDict_SetItem(__pyx_d, __pyx_n_s_json, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
4: import numpy as np
__pyx_t_1 = __Pyx_Import(__pyx_n_s_numpy, 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyDict_SetItem(__pyx_d, __pyx_n_s_np, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
5: import h5py as h5
__pyx_t_1 = __Pyx_Import(__pyx_n_s_h5py, 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyDict_SetItem(__pyx_d, __pyx_n_s_h5, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
6: from astropy import units as u
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7: from astropy.coordinates import Angle, Distance, ICRSCoordinates
__pyx_t_2 = PyList_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(__pyx_n_s_Angle); PyList_SET_ITEM(__pyx_t_2, 0, __pyx_n_s_Angle); __Pyx_GIVEREF(__pyx_n_s_Angle); __Pyx_INCREF(__pyx_n_s_Distance); PyList_SET_ITEM(__pyx_t_2, 1, __pyx_n_s_Distance); __Pyx_GIVEREF(__pyx_n_s_Distance); __Pyx_INCREF(__pyx_n_s_ICRSCoordinates); PyList_SET_ITEM(__pyx_t_2, 2, __pyx_n_s_ICRSCoordinates); __Pyx_GIVEREF(__pyx_n_s_ICRSCoordinates); __pyx_t_1 = __Pyx_Import(__pyx_n_s_astropy_coordinates, __pyx_t_2, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_2 = __Pyx_ImportFrom(__pyx_t_1, __pyx_n_s_Angle); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); if (PyDict_SetItem(__pyx_d, __pyx_n_s_Angle, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_2 = __Pyx_ImportFrom(__pyx_t_1, __pyx_n_s_Distance); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); if (PyDict_SetItem(__pyx_d, __pyx_n_s_Distance, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_2 = __Pyx_ImportFrom(__pyx_t_1, __pyx_n_s_ICRSCoordinates); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); if (PyDict_SetItem(__pyx_d, __pyx_n_s_ICRSCoordinates, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
8: from astropy.cosmology import Planck13, WMAP5
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9: from scipy.spatial import cKDTree
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10:
11: cimport cython
12: cimport numpy as np
13:
14:
15: DTYPE = np.double
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16:
17: ctypedef np.double_t DTYPE_t
18:
19: cdef extern from "math.h":
20: double fabs(double x)
21: double sqrt(double x)
22: double cos(double x)
23: double sin(double x)
24: double acos(double x)
25: double asin(double x)
26: double M_PI
27:
28:
29: cdef double r2dval = 180.0 / M_PI
if (unlikely(M_PI == 0)) {
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#endif
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}
__pyx_v_8complete_r2dval = (180.0 / M_PI);
30: cdef double d2rval = M_PI / 180.0
__pyx_v_8complete_d2rval = (M_PI / 180.0);
31: cdef double third = 1.0 / 3.0
__pyx_v_8complete_third = (1.0 / 3.0);
32:
33:
34: @cython.boundscheck(False)
35: cdef double rad2deg(double rads):
static double __pyx_f_8complete_rad2deg(double __pyx_v_rads) {
double __pyx_r;
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36: return rads * r2dval
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37:
38: @cython.boundscheck(False)
39: cdef double deg2rad(double degs):
static double __pyx_f_8complete_deg2rad(double __pyx_v_degs) {
double __pyx_r;
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40: return degs * d2rval
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41:
42:
43: @cython.boundscheck(False)
44: cdef double [:] radec2xyz(double [:] radecarr):
static __Pyx_memviewslice __pyx_f_8complete_radec2xyz(__Pyx_memviewslice __pyx_v_radecarr) {
double __pyx_v_xyzarr[3];
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45:
46: cdef double[3] xyzarr
47:
48: xyzarr[0] = cos(deg2rad(radecarr[1])) * \
__pyx_t_1 = 1; if (__pyx_t_1 < 0) __pyx_t_1 += __pyx_v_radecarr.shape[0]; /* … */ (__pyx_v_xyzarr[0]) = (cos(__pyx_f_8complete_deg2rad((*((double *) ( /* dim=0 */ (__pyx_v_radecarr.data + __pyx_t_1 * __pyx_v_radecarr.strides[0]) ))))) * cos(__pyx_f_8complete_deg2rad((*((double *) ( /* dim=0 */ (__pyx_v_radecarr.data + __pyx_t_2 * __pyx_v_radecarr.strides[0]) ))))));
49: cos(deg2rad(radecarr[0]))
__pyx_t_2 = 0; if (__pyx_t_2 < 0) __pyx_t_2 += __pyx_v_radecarr.shape[0];
50: xyzarr[1] = cos(deg2rad(radecarr[1])) * \
__pyx_t_3 = 1; if (__pyx_t_3 < 0) __pyx_t_3 += __pyx_v_radecarr.shape[0]; /* … */ (__pyx_v_xyzarr[1]) = (cos(__pyx_f_8complete_deg2rad((*((double *) ( /* dim=0 */ (__pyx_v_radecarr.data + __pyx_t_3 * __pyx_v_radecarr.strides[0]) ))))) * sin(__pyx_f_8complete_deg2rad((*((double *) ( /* dim=0 */ (__pyx_v_radecarr.data + __pyx_t_4 * __pyx_v_radecarr.strides[0]) ))))));
51: sin(deg2rad(radecarr[0]))
__pyx_t_4 = 0; if (__pyx_t_4 < 0) __pyx_t_4 += __pyx_v_radecarr.shape[0];
52: xyzarr[2] = sin(deg2rad(radecarr[1]))
__pyx_t_5 = 1; if (__pyx_t_5 < 0) __pyx_t_5 += __pyx_v_radecarr.shape[0]; (__pyx_v_xyzarr[2]) = sin(__pyx_f_8complete_deg2rad((*((double *) ( /* dim=0 */ (__pyx_v_radecarr.data + __pyx_t_5 * __pyx_v_radecarr.strides[0]) )))));
53:
54: return xyzarr
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55:
56:
57: @cython.boundscheck(False)
58: cdef double central_angle(double [:] coord1, double [:] coord2):
static double __pyx_f_8complete_central_angle(__Pyx_memviewslice __pyx_v_coord1, __Pyx_memviewslice __pyx_v_coord2) {
double __pyx_v_f1;
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59:
60: cdef double f1, f2, dl
61:
62: f1 = deg2rad(coord1[1])
__pyx_t_1 = 1; if (__pyx_t_1 < 0) __pyx_t_1 += __pyx_v_coord1.shape[0]; __pyx_v_f1 = __pyx_f_8complete_deg2rad((*((double *) ( /* dim=0 */ (__pyx_v_coord1.data + __pyx_t_1 * __pyx_v_coord1.strides[0]) ))));
63: f2 = deg2rad(coord2[1])
__pyx_t_2 = 1; if (__pyx_t_2 < 0) __pyx_t_2 += __pyx_v_coord2.shape[0]; __pyx_v_f2 = __pyx_f_8complete_deg2rad((*((double *) ( /* dim=0 */ (__pyx_v_coord2.data + __pyx_t_2 * __pyx_v_coord2.strides[0]) ))));
64:
65: dl = fabs(coord1[0] - coord2[0])
__pyx_t_3 = 0; if (__pyx_t_3 < 0) __pyx_t_3 += __pyx_v_coord1.shape[0]; __pyx_t_4 = 0; if (__pyx_t_4 < 0) __pyx_t_4 += __pyx_v_coord2.shape[0]; __pyx_v_dl = fabs(((*((double *) ( /* dim=0 */ (__pyx_v_coord1.data + __pyx_t_3 * __pyx_v_coord1.strides[0]) ))) - (*((double *) ( /* dim=0 */ (__pyx_v_coord2.data + __pyx_t_4 * __pyx_v_coord2.strides[0]) )))));
66:
67: if dl > 180:
__pyx_t_5 = ((__pyx_v_dl > 180.0) != 0);
if (__pyx_t_5) {
68: dl = deg2rad(dl - 180)
__pyx_v_dl = __pyx_f_8complete_deg2rad((__pyx_v_dl - 180.0));
goto __pyx_L3;
}
/*else*/ {
69: else:
70: dl = deg2rad(dl)
__pyx_v_dl = __pyx_f_8complete_deg2rad(__pyx_v_dl); } __pyx_L3:;
71: # angle is (from wikipedia formula...)
72: return acos(sin(f1) * sin(f2) + cos(f1) * cos(f2) * cos(dl))
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73:
74:
75: @cython.cdivision(True)
76: @cython.boundscheck(False)
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78:
79: cdef double norm
80:
81: cdef np.ndarray[DTYPE_t, ndim=2] good_pts
82: cdef np.ndarray[DTYPE_t, ndim=2] bad_pts
83:
84: cdef int i, rand_i, pt
85: cdef double bad_r, bad_r_deg
86: cdef double zlo, zhi
87:
88: cdef double z_a, z_b
89: cdef double [:] randz
90:
91: cdef double [:] radec
92: cdef double sphdissq
93:
94: cdef double R, l_srch, bad_vol
95: cdef double [:] crc_cen
96: cdef double [:] pt_ang
97: cdef double dis, l
98:
99: Nsph = 10000000
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100: norm = 1. / Nsph
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101:
102: f_good = h5.File("../../dat/out/CMASS/NGC/srch_radec.hdf5")
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107:
108: nbar_dict = json.load(open("../../dat/out/CMASS/NGC/WMAP/nbar_zrange.json"))
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109: zlo = nbar_dict["zlo"]
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110: zhi = nbar_dict["zhi"]
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111:
112: bad_r = acos(1.0 - (M_PI * 9.8544099e-05) / (2 * 180 ** 2))
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113: bad_r_deg = np.rad2deg(bad_r)
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114:
115: WMAP5.__init__(100.0, WMAP5.Om0)
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116: cosmo = WMAP5
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117: comv = cosmo.comoving_distance
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118:
119:
120:
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122: veto_baum = cKDTree(bad_xyz)
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123:
124: rand_i = 0
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125:
126: # t_0 = time.time()
127:
128: # with
129: # open("./test_dat/CMASS/NGC/full_completeness_10mil/volfrac_rad{0}.dat".format(r),
130: # 'a') as f_r:
131:
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133:
134: # print "time: {0} seconds".format(time.time() - t_0)
135: # print " - starting search at radius {0} Mpc".format(r)
136:
137: # Custom zrange for sphere size
138: dis_near = Distance(comv(zlo).value + r, u.Mpc)
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140:
141: z_a = dis_near.compute_z(cosmology=cosmo)
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144:
145: randz = (z_a ** 3 + \
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146: (z_b ** 3 - zlo ** 3) * np.random.rand(Nsph)) ** (1. / 3.)
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147:
148: for i in range(Nsph):
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149:
150: rand_i = rand_i % 999999 # compensate for finite length of mask file
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153:
154: rang = Angle(radec[0], u.deg)
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155: decang = Angle(radec[1], u.deg)
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156:
157: dis = Distance(comv(randz[i]), u.Mpc)
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158:
159: coord = ICRSCoordinates(rang, decang, distance=dis)
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160:
161: sphdissq = coord.x.value * coord.x.value + \
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162: coord.y.value * coord.y.value + \
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163: coord.z.value * coord.z.value
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164:
165: # print "rad: ", r, ", sphere: ", i
166:
167: # Get radius of circular projection of sphere
168: R = asin(r / sqrt(sphdissq))
__pyx_v_R = asin((__pyx_v_r / sqrt(__pyx_v_sphdissq)));
169:
170: # Get coordinates of circle centre on unit sphere
171: crc_cen = radec2xyz(radec)
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__PYX_XDEC_MEMVIEW(&__pyx_v_crc_cen, 1);
__pyx_v_crc_cen = __pyx_t_15;
__pyx_t_15.memview = NULL;
__pyx_t_15.data = NULL;
172:
173: # Compute tree search radius from Cosine rule
174: # (include points extending beyond sphere edge to account for
175: # finite area around bad points)
176: l_srch = sqrt(2. - 2. * cos(R))
__pyx_v_l_srch = sqrt((2. - (2. * cos(__pyx_v_R))));
177:
178: # Run search
179: pierce_l = veto_baum.query_ball_point(crc_cen, l_srch)
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180:
181: bad_vol = 0.
__pyx_v_bad_vol = 0.;
182:
183: R = rad2deg(R) # need in degrees for bad_vol computation
__pyx_v_R = __pyx_f_8complete_rad2deg(__pyx_v_R);
184:
185: for pt in pierce_l:
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198: