[b6627d9] | 1 | # pylint: disable=invalid-name |
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[51f14603] | 2 | """ |
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[fd5ac0d] | 3 | SAS generic computation and sld file readers |
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[51f14603] | 4 | """ |
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[9e531f2] | 5 | import sas.sascalc.calculator.core.sld2i as mod |
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[d2fd8fc] | 6 | from sas.sascalc.calculator.BaseComponent import BaseComponent |
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[51f14603] | 7 | from periodictable import formula |
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| 8 | from periodictable import nsf |
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[9a5097c] | 9 | import numpy as np |
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[51f14603] | 10 | import os |
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| 11 | import copy |
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[b6627d9] | 12 | import sys |
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| 13 | import logging |
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[51f14603] | 14 | |
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[463e7ffc] | 15 | logger = logging.getLogger(__name__) |
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[c155a16] | 16 | |
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[e3f77d8b] | 17 | MFACTOR_AM = 2.853E-12 |
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| 18 | MFACTOR_MT = 2.3164E-9 |
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[51f14603] | 19 | METER2ANG = 1.0E+10 |
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| 20 | #Avogadro constant [1/mol] |
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| 21 | NA = 6.02214129e+23 |
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| 22 | |
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| 23 | def mag2sld(mag, v_unit=None): |
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| 24 | """ |
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| 25 | Convert magnetization to magnatic SLD |
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| 26 | sldm = Dm * mag where Dm = gamma * classical elec. radius/(2*Bohr magneton) |
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| 27 | Dm ~ 2.853E-12 [A^(-2)] ==> Shouldn't be 2.90636E-12 [A^(-2)]??? |
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[e3f77d8b] | 28 | """ |
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[51f14603] | 29 | if v_unit == "A/m": |
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[e3f77d8b] | 30 | factor = MFACTOR_AM |
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[51f14603] | 31 | elif v_unit == "mT": |
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[e3f77d8b] | 32 | factor = MFACTOR_MT |
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[51f14603] | 33 | else: |
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| 34 | raise ValueError, "Invalid valueunit" |
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| 35 | sld_m = factor * mag |
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| 36 | return sld_m |
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| 37 | |
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| 38 | def transform_center(pos_x, pos_y, pos_z): |
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| 39 | """ |
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[e3f77d8b] | 40 | re-center |
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[51f14603] | 41 | :return: posx, posy, posz [arrays] |
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[e3f77d8b] | 42 | """ |
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[51f14603] | 43 | posx = pos_x - (min(pos_x) + max(pos_x)) / 2.0 |
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| 44 | posy = pos_y - (min(pos_y) + max(pos_y)) / 2.0 |
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[e3f77d8b] | 45 | posz = pos_z - (min(pos_z) + max(pos_z)) / 2.0 |
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| 46 | return posx, posy, posz |
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[51f14603] | 47 | |
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| 48 | class GenSAS(BaseComponent): |
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| 49 | """ |
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| 50 | Generic SAS computation Model based on sld (n & m) arrays |
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| 51 | """ |
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| 52 | def __init__(self): |
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| 53 | """ |
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| 54 | Init |
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| 55 | :Params sld_data: MagSLD object |
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| 56 | """ |
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| 57 | # Initialize BaseComponent |
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| 58 | BaseComponent.__init__(self) |
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| 59 | self.sld_data = None |
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| 60 | self.data_pos_unit = None |
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| 61 | self.data_x = None |
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| 62 | self.data_y = None |
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| 63 | self.data_z = None |
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| 64 | self.data_sldn = None |
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| 65 | self.data_mx = None |
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| 66 | self.data_my = None |
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| 67 | self.data_mz = None |
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| 68 | self.data_vol = None #[A^3] |
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| 69 | self.is_avg = False |
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| 70 | ## Name of the model |
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| 71 | self.name = "GenSAS" |
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| 72 | ## Define parameters |
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| 73 | self.params = {} |
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[e3f77d8b] | 74 | self.params['scale'] = 1.0 |
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| 75 | self.params['background'] = 0.0 |
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| 76 | self.params['solvent_SLD'] = 0.0 |
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[51f14603] | 77 | self.params['total_volume'] = 1.0 |
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[e3f77d8b] | 78 | self.params['Up_frac_in'] = 1.0 |
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| 79 | self.params['Up_frac_out'] = 1.0 |
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| 80 | self.params['Up_theta'] = 0.0 |
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[51f14603] | 81 | self.description = 'GenSAS' |
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| 82 | ## Parameter details [units, min, max] |
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| 83 | self.details = {} |
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[9a5097c] | 84 | self.details['scale'] = ['', 0.0, np.inf] |
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| 85 | self.details['background'] = ['[1/cm]', 0.0, np.inf] |
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| 86 | self.details['solvent_SLD'] = ['1/A^(2)', -np.inf, np.inf] |
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| 87 | self.details['total_volume'] = ['A^(3)', 0.0, np.inf] |
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[cb4ef58] | 88 | self.details['Up_frac_in'] = ['[u/(u+d)]', 0.0, 1.0] |
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| 89 | self.details['Up_frac_out'] = ['[u/(u+d)]', 0.0, 1.0] |
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[9a5097c] | 90 | self.details['Up_theta'] = ['[deg]', -np.inf, np.inf] |
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[51f14603] | 91 | # fixed parameters |
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| 92 | self.fixed = [] |
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[e3f77d8b] | 93 | |
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| 94 | def set_pixel_volumes(self, volume): |
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[51f14603] | 95 | """ |
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| 96 | Set the volume of a pixel in (A^3) unit |
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| 97 | :Param volume: pixel volume [float] |
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| 98 | """ |
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| 99 | if self.data_vol == None: |
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| 100 | raise |
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| 101 | self.data_vol = volume |
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[e3f77d8b] | 102 | |
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| 103 | def set_is_avg(self, is_avg=False): |
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[51f14603] | 104 | """ |
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| 105 | Sets is_avg: [bool] |
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| 106 | """ |
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| 107 | self.is_avg = is_avg |
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[e3f77d8b] | 108 | |
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[51f14603] | 109 | def _gen(self, x, y, i): |
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| 110 | """ |
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| 111 | Evaluate the function |
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| 112 | :Param x: array of x-values |
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| 113 | :Param y: array of y-values |
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[e3f77d8b] | 114 | :Param i: array of initial i-value |
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[51f14603] | 115 | :return: function value |
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| 116 | """ |
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| 117 | pos_x = self.data_x |
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| 118 | pos_y = self.data_y |
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| 119 | pos_z = self.data_z |
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| 120 | len_x = len(pos_x) |
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| 121 | if self.is_avg == None: |
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| 122 | len_x *= -1 |
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| 123 | pos_x, pos_y, pos_z = transform_center(pos_x, pos_y, pos_z) |
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| 124 | len_q = len(x) |
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| 125 | sldn = copy.deepcopy(self.data_sldn) |
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| 126 | sldn -= self.params['solvent_SLD'] |
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[e3f77d8b] | 127 | model = mod.new_GenI(len_x, pos_x, pos_y, pos_z, |
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| 128 | sldn, self.data_mx, self.data_my, |
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[51f14603] | 129 | self.data_mz, self.data_vol, |
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[e3f77d8b] | 130 | self.params['Up_frac_in'], |
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| 131 | self.params['Up_frac_out'], |
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[51f14603] | 132 | self.params['Up_theta']) |
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| 133 | if y == []: |
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| 134 | mod.genicom(model, len_q, x, i) |
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| 135 | else: |
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| 136 | mod.genicomXY(model, len_q, x, y, i) |
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| 137 | vol_correction = self.data_total_volume / self.params['total_volume'] |
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| 138 | return self.params['scale'] * vol_correction * i + \ |
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| 139 | self.params['background'] |
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[e3f77d8b] | 140 | |
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| 141 | def set_sld_data(self, sld_data=None): |
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[51f14603] | 142 | """ |
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| 143 | Sets sld_data |
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| 144 | """ |
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| 145 | self.sld_data = sld_data |
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| 146 | self.data_pos_unit = sld_data.pos_unit |
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| 147 | self.data_x = sld_data.pos_x |
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| 148 | self.data_y = sld_data.pos_y |
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| 149 | self.data_z = sld_data.pos_z |
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| 150 | self.data_sldn = sld_data.sld_n |
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| 151 | self.data_mx = sld_data.sld_mx |
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| 152 | self.data_my = sld_data.sld_my |
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| 153 | self.data_mz = sld_data.sld_mz |
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| 154 | self.data_vol = sld_data.vol_pix |
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| 155 | self.data_total_volume = sum(sld_data.vol_pix) |
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| 156 | self.params['total_volume'] = sum(sld_data.vol_pix) |
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[e3f77d8b] | 157 | |
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[51f14603] | 158 | def getProfile(self): |
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| 159 | """ |
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[e3f77d8b] | 160 | Get SLD profile |
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[51f14603] | 161 | : return: sld_data |
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| 162 | """ |
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| 163 | return self.sld_data |
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[e3f77d8b] | 164 | |
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| 165 | def run(self, x=0.0): |
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| 166 | """ |
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[51f14603] | 167 | Evaluate the model |
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| 168 | :param x: simple value |
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| 169 | :return: (I value) |
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| 170 | """ |
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| 171 | if x.__class__.__name__ == 'list': |
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| 172 | if len(x[1]) > 0: |
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| 173 | msg = "Not a 1D." |
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| 174 | raise ValueError, msg |
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[9a5097c] | 175 | i_out = np.zeros_like(x[0]) |
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[51f14603] | 176 | # 1D I is found at y =0 in the 2D pattern |
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[e3f77d8b] | 177 | out = self._gen(x[0], [], i_out) |
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[51f14603] | 178 | return out |
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| 179 | else: |
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| 180 | msg = "Q must be given as list of qx's and qy's" |
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| 181 | raise ValueError, msg |
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[e3f77d8b] | 182 | |
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| 183 | def runXY(self, x=0.0): |
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| 184 | """ |
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[51f14603] | 185 | Evaluate the model |
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| 186 | :param x: simple value |
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| 187 | :return: I value |
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| 188 | :Use this runXY() for the computation |
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| 189 | """ |
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| 190 | if x.__class__.__name__ == 'list': |
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[9a5097c] | 191 | i_out = np.zeros_like(x[0]) |
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[51f14603] | 192 | out = self._gen(x[0], x[1], i_out) |
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| 193 | return out |
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| 194 | else: |
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| 195 | msg = "Q must be given as list of qx's and qy's" |
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| 196 | raise ValueError, msg |
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[e3f77d8b] | 197 | |
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[51f14603] | 198 | def evalDistribution(self, qdist): |
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| 199 | """ |
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| 200 | Evaluate a distribution of q-values. |
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[ac7be54] | 201 | |
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| 202 | :param qdist: ndarray of scalar q-values (for 1D) or list [qx,qy] |
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| 203 | where qx,qy are 1D ndarrays (for 2D). |
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[51f14603] | 204 | """ |
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| 205 | if qdist.__class__.__name__ == 'list': |
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| 206 | if len(qdist[1]) < 1: |
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| 207 | out = self.run(qdist) |
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| 208 | else: |
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| 209 | out = self.runXY(qdist) |
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| 210 | return out |
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| 211 | else: |
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| 212 | mesg = "evalDistribution is expecting an ndarray of " |
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| 213 | mesg += "a list [qx,qy] where qx,qy are arrays." |
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| 214 | raise RuntimeError, mesg |
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[e3f77d8b] | 215 | |
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| 216 | class OMF2SLD(object): |
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[51f14603] | 217 | """ |
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| 218 | Convert OMFData to MAgData |
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| 219 | """ |
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[e3f77d8b] | 220 | def __init__(self): |
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[51f14603] | 221 | """ |
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| 222 | Init |
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| 223 | """ |
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| 224 | self.pos_x = None |
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| 225 | self.pos_y = None |
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| 226 | self.pos_z = None |
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| 227 | self.mx = None |
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| 228 | self.my = None |
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| 229 | self.mz = None |
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| 230 | self.sld_n = None |
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| 231 | self.vol_pix = None |
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| 232 | self.output = None |
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| 233 | self.omfdata = None |
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[e3f77d8b] | 234 | |
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[51f14603] | 235 | def set_data(self, omfdata, shape='rectangular'): |
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| 236 | """ |
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| 237 | Set all data |
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| 238 | """ |
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| 239 | self.omfdata = omfdata |
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| 240 | length = int(omfdata.xnodes * omfdata.ynodes * omfdata.znodes) |
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[9a5097c] | 241 | pos_x = np.arange(omfdata.xmin, |
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[e3f77d8b] | 242 | omfdata.xnodes*omfdata.xstepsize + omfdata.xmin, |
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[51f14603] | 243 | omfdata.xstepsize) |
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[9a5097c] | 244 | pos_y = np.arange(omfdata.ymin, |
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[e3f77d8b] | 245 | omfdata.ynodes*omfdata.ystepsize + omfdata.ymin, |
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[51f14603] | 246 | omfdata.ystepsize) |
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[9a5097c] | 247 | pos_z = np.arange(omfdata.zmin, |
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[e3f77d8b] | 248 | omfdata.znodes*omfdata.zstepsize + omfdata.zmin, |
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[51f14603] | 249 | omfdata.zstepsize) |
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[9a5097c] | 250 | self.pos_x = np.tile(pos_x, int(omfdata.ynodes * omfdata.znodes)) |
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[51f14603] | 251 | self.pos_y = pos_y.repeat(int(omfdata.xnodes)) |
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[9a5097c] | 252 | self.pos_y = np.tile(self.pos_y, int(omfdata.znodes)) |
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[51f14603] | 253 | self.pos_z = pos_z.repeat(int(omfdata.xnodes * omfdata.ynodes)) |
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| 254 | self.mx = omfdata.mx |
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| 255 | self.my = omfdata.my |
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| 256 | self.mz = omfdata.mz |
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[9a5097c] | 257 | self.sld_n = np.zeros(length) |
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[e3f77d8b] | 258 | |
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[51f14603] | 259 | if omfdata.mx == None: |
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[9a5097c] | 260 | self.mx = np.zeros(length) |
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[51f14603] | 261 | if omfdata.my == None: |
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[9a5097c] | 262 | self.my = np.zeros(length) |
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[51f14603] | 263 | if omfdata.mz == None: |
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[9a5097c] | 264 | self.mz = np.zeros(length) |
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[e3f77d8b] | 265 | |
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[51f14603] | 266 | self._check_data_length(length) |
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| 267 | self.remove_null_points(False, False) |
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[9a5097c] | 268 | mask = np.ones(len(self.sld_n), dtype=bool) |
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[51f14603] | 269 | if shape.lower() == 'ellipsoid': |
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| 270 | try: |
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| 271 | # Pixel (step) size included |
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| 272 | x_c = max(self.pos_x) + min(self.pos_x) |
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| 273 | y_c = max(self.pos_y) + min(self.pos_y) |
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| 274 | z_c = max(self.pos_z) + min(self.pos_z) |
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| 275 | x_d = max(self.pos_x) - min(self.pos_x) |
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| 276 | y_d = max(self.pos_y) - min(self.pos_y) |
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| 277 | z_d = max(self.pos_z) - min(self.pos_z) |
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| 278 | x_r = (x_d + omfdata.xstepsize) / 2.0 |
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| 279 | y_r = (y_d + omfdata.ystepsize) / 2.0 |
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| 280 | z_r = (z_d + omfdata.zstepsize) / 2.0 |
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| 281 | x_dir2 = ((self.pos_x - x_c / 2.0) / x_r) |
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| 282 | x_dir2 *= x_dir2 |
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| 283 | y_dir2 = ((self.pos_y - y_c / 2.0) / y_r) |
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| 284 | y_dir2 *= y_dir2 |
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| 285 | z_dir2 = ((self.pos_z - z_c / 2.0) / z_r) |
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| 286 | z_dir2 *= z_dir2 |
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| 287 | mask = (x_dir2 + y_dir2 + z_dir2) <= 1.0 |
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| 288 | except: |
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[c155a16] | 289 | logger.error(sys.exc_value) |
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[e3f77d8b] | 290 | self.output = MagSLD(self.pos_x[mask], self.pos_y[mask], |
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| 291 | self.pos_z[mask], self.sld_n[mask], |
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[51f14603] | 292 | self.mx[mask], self.my[mask], self.mz[mask]) |
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| 293 | self.output.set_pix_type('pixel') |
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| 294 | self.output.set_pixel_symbols('pixel') |
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[e3f77d8b] | 295 | |
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[51f14603] | 296 | def get_omfdata(self): |
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| 297 | """ |
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| 298 | Return all data |
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| 299 | """ |
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| 300 | return self.omfdata |
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[e3f77d8b] | 301 | |
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[51f14603] | 302 | def get_output(self): |
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| 303 | """ |
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| 304 | Return output |
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| 305 | """ |
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| 306 | return self.output |
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[e3f77d8b] | 307 | |
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[51f14603] | 308 | def _check_data_length(self, length): |
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| 309 | """ |
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| 310 | Check if the data lengths are consistent |
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| 311 | :Params length: data length |
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| 312 | """ |
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| 313 | msg = "Error: Inconsistent data length." |
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| 314 | if len(self.pos_x) != length: |
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| 315 | raise ValueError, msg |
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| 316 | if len(self.pos_y) != length: |
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| 317 | raise ValueError, msg |
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| 318 | if len(self.pos_z) != length: |
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| 319 | raise ValueError, msg |
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| 320 | if len(self.mx) != length: |
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| 321 | raise ValueError, msg |
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| 322 | if len(self.my) != length: |
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| 323 | raise ValueError, msg |
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| 324 | if len(self.mz) != length: |
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| 325 | raise ValueError, msg |
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[e3f77d8b] | 326 | |
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[51f14603] | 327 | def remove_null_points(self, remove=False, recenter=False): |
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| 328 | """ |
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| 329 | Removes any mx, my, and mz = 0 points |
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| 330 | """ |
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| 331 | if remove: |
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[9a5097c] | 332 | is_nonzero = (np.fabs(self.mx) + np.fabs(self.my) + |
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| 333 | np.fabs(self.mz)).nonzero() |
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[e3f77d8b] | 334 | if len(is_nonzero[0]) > 0: |
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[51f14603] | 335 | self.pos_x = self.pos_x[is_nonzero] |
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| 336 | self.pos_y = self.pos_y[is_nonzero] |
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| 337 | self.pos_z = self.pos_z[is_nonzero] |
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| 338 | self.sld_n = self.sld_n[is_nonzero] |
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| 339 | self.mx = self.mx[is_nonzero] |
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| 340 | self.my = self.my[is_nonzero] |
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| 341 | self.mz = self.mz[is_nonzero] |
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| 342 | if recenter: |
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| 343 | self.pos_x -= (min(self.pos_x) + max(self.pos_x)) / 2.0 |
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| 344 | self.pos_y -= (min(self.pos_y) + max(self.pos_y)) / 2.0 |
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| 345 | self.pos_z -= (min(self.pos_z) + max(self.pos_z)) / 2.0 |
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[e3f77d8b] | 346 | |
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[51f14603] | 347 | def get_magsld(self): |
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| 348 | """ |
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| 349 | return MagSLD |
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| 350 | """ |
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| 351 | return self.output |
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[e3f77d8b] | 352 | |
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| 353 | |
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| 354 | class OMFReader(object): |
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[51f14603] | 355 | """ |
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| 356 | Class to load omf/ascii files (3 columns w/header). |
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| 357 | """ |
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| 358 | ## File type |
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| 359 | type_name = "OMF ASCII" |
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[e3f77d8b] | 360 | |
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[51f14603] | 361 | ## Wildcards |
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| 362 | type = ["OMF files (*.OMF, *.omf)|*.omf"] |
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| 363 | ## List of allowed extensions |
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| 364 | ext = ['.omf', '.OMF'] |
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[e3f77d8b] | 365 | |
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[51f14603] | 366 | def read(self, path): |
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| 367 | """ |
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| 368 | Load data file |
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| 369 | :param path: file path |
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| 370 | :return: x, y, z, sld_n, sld_mx, sld_my, sld_mz |
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| 371 | """ |
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| 372 | desc = "" |
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[9a5097c] | 373 | mx = np.zeros(0) |
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| 374 | my = np.zeros(0) |
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| 375 | mz = np.zeros(0) |
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[51f14603] | 376 | try: |
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| 377 | input_f = open(path, 'rb') |
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| 378 | buff = input_f.read() |
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| 379 | lines = buff.split('\n') |
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| 380 | input_f.close() |
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| 381 | output = OMFData() |
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| 382 | valueunit = None |
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| 383 | for line in lines: |
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| 384 | toks = line.split() |
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| 385 | # Read data |
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| 386 | try: |
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| 387 | _mx = float(toks[0]) |
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| 388 | _my = float(toks[1]) |
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| 389 | _mz = float(toks[2]) |
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| 390 | _mx = mag2sld(_mx, valueunit) |
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| 391 | _my = mag2sld(_my, valueunit) |
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| 392 | _mz = mag2sld(_mz, valueunit) |
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[9a5097c] | 393 | mx = np.append(mx, _mx) |
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| 394 | my = np.append(my, _my) |
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| 395 | mz = np.append(mz, _mz) |
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[51f14603] | 396 | except: |
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| 397 | # Skip non-data lines |
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[c155a16] | 398 | logger.error(sys.exc_value) |
---|
[51f14603] | 399 | #Reading Header; Segment count ignored |
---|
| 400 | s_line = line.split(":", 1) |
---|
| 401 | if s_line[0].lower().count("oommf") > 0: |
---|
| 402 | oommf = s_line[1].lstrip() |
---|
| 403 | if s_line[0].lower().count("title") > 0: |
---|
| 404 | title = s_line[1].lstrip() |
---|
| 405 | if s_line[0].lower().count("desc") > 0: |
---|
| 406 | desc += s_line[1].lstrip() |
---|
| 407 | desc += '\n' |
---|
| 408 | if s_line[0].lower().count("meshtype") > 0: |
---|
| 409 | meshtype = s_line[1].lstrip() |
---|
| 410 | if s_line[0].lower().count("meshunit") > 0: |
---|
| 411 | meshunit = s_line[1].lstrip() |
---|
| 412 | if meshunit.count("m") < 1: |
---|
| 413 | msg = "Error: \n" |
---|
| 414 | msg += "We accept only m as meshunit" |
---|
| 415 | raise ValueError, msg |
---|
| 416 | if s_line[0].lower().count("xbase") > 0: |
---|
| 417 | xbase = s_line[1].lstrip() |
---|
| 418 | if s_line[0].lower().count("ybase") > 0: |
---|
| 419 | ybase = s_line[1].lstrip() |
---|
| 420 | if s_line[0].lower().count("zbase") > 0: |
---|
| 421 | zbase = s_line[1].lstrip() |
---|
| 422 | if s_line[0].lower().count("xstepsize") > 0: |
---|
| 423 | xstepsize = s_line[1].lstrip() |
---|
| 424 | if s_line[0].lower().count("ystepsize") > 0: |
---|
| 425 | ystepsize = s_line[1].lstrip() |
---|
| 426 | if s_line[0].lower().count("zstepsize") > 0: |
---|
| 427 | zstepsize = s_line[1].lstrip() |
---|
| 428 | if s_line[0].lower().count("xnodes") > 0: |
---|
| 429 | xnodes = s_line[1].lstrip() |
---|
| 430 | if s_line[0].lower().count("ynodes") > 0: |
---|
| 431 | ynodes = s_line[1].lstrip() |
---|
| 432 | if s_line[0].lower().count("znodes") > 0: |
---|
| 433 | znodes = s_line[1].lstrip() |
---|
| 434 | if s_line[0].lower().count("xmin") > 0: |
---|
| 435 | xmin = s_line[1].lstrip() |
---|
| 436 | if s_line[0].lower().count("ymin") > 0: |
---|
| 437 | ymin = s_line[1].lstrip() |
---|
| 438 | if s_line[0].lower().count("zmin") > 0: |
---|
| 439 | zmin = s_line[1].lstrip() |
---|
| 440 | if s_line[0].lower().count("xmax") > 0: |
---|
| 441 | xmax = s_line[1].lstrip() |
---|
| 442 | if s_line[0].lower().count("ymax") > 0: |
---|
| 443 | ymax = s_line[1].lstrip() |
---|
| 444 | if s_line[0].lower().count("zmax") > 0: |
---|
| 445 | zmax = s_line[1].lstrip() |
---|
| 446 | if s_line[0].lower().count("valueunit") > 0: |
---|
| 447 | valueunit = s_line[1].lstrip().rstrip() |
---|
| 448 | if s_line[0].lower().count("valuemultiplier") > 0: |
---|
| 449 | valuemultiplier = s_line[1].lstrip() |
---|
| 450 | if s_line[0].lower().count("valuerangeminmag") > 0: |
---|
| 451 | valuerangeminmag = s_line[1].lstrip() |
---|
| 452 | if s_line[0].lower().count("valuerangemaxmag") > 0: |
---|
| 453 | valuerangemaxmag = s_line[1].lstrip() |
---|
| 454 | if s_line[0].lower().count("end") > 0: |
---|
| 455 | output.filename = os.path.basename(path) |
---|
| 456 | output.oommf = oommf |
---|
| 457 | output.title = title |
---|
| 458 | output.desc = desc |
---|
| 459 | output.meshtype = meshtype |
---|
| 460 | output.xbase = float(xbase) * METER2ANG |
---|
| 461 | output.ybase = float(ybase) * METER2ANG |
---|
| 462 | output.zbase = float(zbase) * METER2ANG |
---|
| 463 | output.xstepsize = float(xstepsize) * METER2ANG |
---|
| 464 | output.ystepsize = float(ystepsize) * METER2ANG |
---|
| 465 | output.zstepsize = float(zstepsize) * METER2ANG |
---|
| 466 | output.xnodes = float(xnodes) |
---|
| 467 | output.ynodes = float(ynodes) |
---|
| 468 | output.znodes = float(znodes) |
---|
| 469 | output.xmin = float(xmin) * METER2ANG |
---|
| 470 | output.ymin = float(ymin) * METER2ANG |
---|
| 471 | output.zmin = float(zmin) * METER2ANG |
---|
| 472 | output.xmax = float(xmax) * METER2ANG |
---|
| 473 | output.ymax = float(ymax) * METER2ANG |
---|
| 474 | output.zmax = float(zmax) * METER2ANG |
---|
| 475 | output.valuemultiplier = valuemultiplier |
---|
| 476 | output.valuerangeminmag = mag2sld(float(valuerangeminmag), \ |
---|
| 477 | valueunit) |
---|
| 478 | output.valuerangemaxmag = mag2sld(float(valuerangemaxmag), \ |
---|
| 479 | valueunit) |
---|
| 480 | output.set_m(mx, my, mz) |
---|
| 481 | return output |
---|
| 482 | except: |
---|
| 483 | msg = "%s is not supported: \n" % path |
---|
| 484 | msg += "We accept only Text format OMF file." |
---|
| 485 | raise RuntimeError, msg |
---|
| 486 | |
---|
[e3f77d8b] | 487 | class PDBReader(object): |
---|
[51f14603] | 488 | """ |
---|
| 489 | PDB reader class: limited for reading the lines starting with 'ATOM' |
---|
| 490 | """ |
---|
| 491 | type_name = "PDB" |
---|
| 492 | ## Wildcards |
---|
| 493 | type = ["pdb files (*.PDB, *.pdb)|*.pdb"] |
---|
| 494 | ## List of allowed extensions |
---|
[e3f77d8b] | 495 | ext = ['.pdb', '.PDB'] |
---|
| 496 | |
---|
[51f14603] | 497 | def read(self, path): |
---|
| 498 | """ |
---|
| 499 | Load data file |
---|
[e3f77d8b] | 500 | |
---|
[51f14603] | 501 | :param path: file path |
---|
| 502 | :return: MagSLD |
---|
| 503 | :raise RuntimeError: when the file can't be opened |
---|
| 504 | """ |
---|
[9a5097c] | 505 | pos_x = np.zeros(0) |
---|
| 506 | pos_y = np.zeros(0) |
---|
| 507 | pos_z = np.zeros(0) |
---|
| 508 | sld_n = np.zeros(0) |
---|
| 509 | sld_mx = np.zeros(0) |
---|
| 510 | sld_my = np.zeros(0) |
---|
| 511 | sld_mz = np.zeros(0) |
---|
| 512 | vol_pix = np.zeros(0) |
---|
| 513 | pix_symbol = np.zeros(0) |
---|
[51f14603] | 514 | x_line = [] |
---|
| 515 | y_line = [] |
---|
| 516 | z_line = [] |
---|
| 517 | x_lines = [] |
---|
| 518 | y_lines = [] |
---|
[e3f77d8b] | 519 | z_lines = [] |
---|
[51f14603] | 520 | try: |
---|
| 521 | input_f = open(path, 'rb') |
---|
| 522 | buff = input_f.read() |
---|
| 523 | lines = buff.split('\n') |
---|
| 524 | input_f.close() |
---|
| 525 | num = 0 |
---|
| 526 | for line in lines: |
---|
| 527 | try: |
---|
| 528 | # check if line starts with "ATOM" |
---|
| 529 | if line[0:6].strip().count('ATM') > 0 or \ |
---|
| 530 | line[0:6].strip() == 'ATOM': |
---|
| 531 | # define fields of interest |
---|
| 532 | atom_name = line[12:16].strip() |
---|
| 533 | try: |
---|
| 534 | float(line[12]) |
---|
| 535 | atom_name = atom_name[1].upper() |
---|
| 536 | except: |
---|
| 537 | if len(atom_name) == 4: |
---|
| 538 | atom_name = atom_name[0].upper() |
---|
[e3f77d8b] | 539 | elif line[12] != ' ': |
---|
[51f14603] | 540 | atom_name = atom_name[0].upper() + \ |
---|
[e3f77d8b] | 541 | atom_name[1].lower() |
---|
[51f14603] | 542 | else: |
---|
| 543 | atom_name = atom_name[0].upper() |
---|
| 544 | _pos_x = float(line[30:38].strip()) |
---|
| 545 | _pos_y = float(line[38:46].strip()) |
---|
| 546 | _pos_z = float(line[46:54].strip()) |
---|
[9a5097c] | 547 | pos_x = np.append(pos_x, _pos_x) |
---|
| 548 | pos_y = np.append(pos_y, _pos_y) |
---|
| 549 | pos_z = np.append(pos_z, _pos_z) |
---|
[51f14603] | 550 | try: |
---|
| 551 | val = nsf.neutron_sld(atom_name)[0] |
---|
| 552 | # sld in Ang^-2 unit |
---|
| 553 | val *= 1.0e-6 |
---|
[9a5097c] | 554 | sld_n = np.append(sld_n, val) |
---|
[51f14603] | 555 | atom = formula(atom_name) |
---|
| 556 | # cm to A units |
---|
| 557 | vol = 1.0e+24 * atom.mass / atom.density / NA |
---|
[9a5097c] | 558 | vol_pix = np.append(vol_pix, vol) |
---|
[51f14603] | 559 | except: |
---|
| 560 | print "Error: set the sld of %s to zero"% atom_name |
---|
[9a5097c] | 561 | sld_n = np.append(sld_n, 0.0) |
---|
| 562 | sld_mx = np.append(sld_mx, 0) |
---|
| 563 | sld_my = np.append(sld_my, 0) |
---|
| 564 | sld_mz = np.append(sld_mz, 0) |
---|
| 565 | pix_symbol = np.append(pix_symbol, atom_name) |
---|
[e3f77d8b] | 566 | elif line[0:6].strip().count('CONECT') > 0: |
---|
[51f14603] | 567 | toks = line.split() |
---|
[e3f77d8b] | 568 | num = int(toks[1]) - 1 |
---|
| 569 | val_list = [] |
---|
[51f14603] | 570 | for val in toks[2:]: |
---|
| 571 | try: |
---|
| 572 | int_val = int(val) |
---|
| 573 | except: |
---|
| 574 | break |
---|
| 575 | if int_val == 0: |
---|
| 576 | break |
---|
| 577 | val_list.append(int_val) |
---|
[e3f77d8b] | 578 | #need val_list ordered |
---|
[51f14603] | 579 | for val in val_list: |
---|
| 580 | index = val - 1 |
---|
| 581 | if (pos_x[index], pos_x[num]) in x_line and \ |
---|
| 582 | (pos_y[index], pos_y[num]) in y_line and \ |
---|
| 583 | (pos_z[index], pos_z[num]) in z_line: |
---|
| 584 | continue |
---|
| 585 | x_line.append((pos_x[num], pos_x[index])) |
---|
| 586 | y_line.append((pos_y[num], pos_y[index])) |
---|
| 587 | z_line.append((pos_z[num], pos_z[index])) |
---|
| 588 | if len(x_line) > 0: |
---|
[e3f77d8b] | 589 | x_lines.append(x_line) |
---|
[51f14603] | 590 | y_lines.append(y_line) |
---|
[e3f77d8b] | 591 | z_lines.append(z_line) |
---|
[51f14603] | 592 | except: |
---|
[c155a16] | 593 | logger.error(sys.exc_value) |
---|
[e3f77d8b] | 594 | |
---|
[51f14603] | 595 | output = MagSLD(pos_x, pos_y, pos_z, sld_n, sld_mx, sld_my, sld_mz) |
---|
| 596 | output.set_conect_lines(x_line, y_line, z_line) |
---|
| 597 | output.filename = os.path.basename(path) |
---|
| 598 | output.set_pix_type('atom') |
---|
| 599 | output.set_pixel_symbols(pix_symbol) |
---|
| 600 | output.set_nodes() |
---|
| 601 | output.set_pixel_volumes(vol_pix) |
---|
| 602 | output.sld_unit = '1/A^(2)' |
---|
| 603 | return output |
---|
| 604 | except: |
---|
[e3f77d8b] | 605 | raise RuntimeError, "%s is not a sld file" % path |
---|
[51f14603] | 606 | |
---|
| 607 | def write(self, path, data): |
---|
| 608 | """ |
---|
| 609 | Write |
---|
| 610 | """ |
---|
| 611 | print "Not implemented... " |
---|
| 612 | |
---|
[e3f77d8b] | 613 | class SLDReader(object): |
---|
[51f14603] | 614 | """ |
---|
| 615 | Class to load ascii files (7 columns). |
---|
| 616 | """ |
---|
| 617 | ## File type |
---|
| 618 | type_name = "SLD ASCII" |
---|
| 619 | ## Wildcards |
---|
| 620 | type = ["sld files (*.SLD, *.sld)|*.sld", |
---|
| 621 | "txt files (*.TXT, *.txt)|*.txt", |
---|
| 622 | "all files (*.*)|*.*"] |
---|
| 623 | ## List of allowed extensions |
---|
| 624 | ext = ['.sld', '.SLD', '.txt', '.TXT', '.*'] |
---|
| 625 | def read(self, path): |
---|
| 626 | """ |
---|
| 627 | Load data file |
---|
| 628 | :param path: file path |
---|
| 629 | :return MagSLD: x, y, z, sld_n, sld_mx, sld_my, sld_mz |
---|
| 630 | :raise RuntimeError: when the file can't be opened |
---|
| 631 | :raise ValueError: when the length of the data vectors are inconsistent |
---|
| 632 | """ |
---|
| 633 | try: |
---|
[9a5097c] | 634 | pos_x = np.zeros(0) |
---|
| 635 | pos_y = np.zeros(0) |
---|
| 636 | pos_z = np.zeros(0) |
---|
| 637 | sld_n = np.zeros(0) |
---|
| 638 | sld_mx = np.zeros(0) |
---|
| 639 | sld_my = np.zeros(0) |
---|
| 640 | sld_mz = np.zeros(0) |
---|
[51f14603] | 641 | try: |
---|
| 642 | # Use numpy to speed up loading |
---|
[9a5097c] | 643 | input_f = np.loadtxt(path, dtype='float', skiprows=1, |
---|
[51f14603] | 644 | ndmin=1, unpack=True) |
---|
[9a5097c] | 645 | pos_x = np.array(input_f[0]) |
---|
| 646 | pos_y = np.array(input_f[1]) |
---|
| 647 | pos_z = np.array(input_f[2]) |
---|
| 648 | sld_n = np.array(input_f[3]) |
---|
| 649 | sld_mx = np.array(input_f[4]) |
---|
| 650 | sld_my = np.array(input_f[5]) |
---|
| 651 | sld_mz = np.array(input_f[6]) |
---|
[51f14603] | 652 | ncols = len(input_f) |
---|
| 653 | if ncols == 8: |
---|
[9a5097c] | 654 | vol_pix = np.array(input_f[7]) |
---|
[51f14603] | 655 | elif ncols == 7: |
---|
[e3f77d8b] | 656 | vol_pix = None |
---|
[51f14603] | 657 | except: |
---|
| 658 | # For older version of numpy |
---|
| 659 | input_f = open(path, 'rb') |
---|
| 660 | buff = input_f.read() |
---|
| 661 | lines = buff.split('\n') |
---|
| 662 | input_f.close() |
---|
| 663 | for line in lines: |
---|
| 664 | toks = line.split() |
---|
| 665 | try: |
---|
| 666 | _pos_x = float(toks[0]) |
---|
| 667 | _pos_y = float(toks[1]) |
---|
| 668 | _pos_z = float(toks[2]) |
---|
| 669 | _sld_n = float(toks[3]) |
---|
| 670 | _sld_mx = float(toks[4]) |
---|
| 671 | _sld_my = float(toks[5]) |
---|
| 672 | _sld_mz = float(toks[6]) |
---|
[9a5097c] | 673 | pos_x = np.append(pos_x, _pos_x) |
---|
| 674 | pos_y = np.append(pos_y, _pos_y) |
---|
| 675 | pos_z = np.append(pos_z, _pos_z) |
---|
| 676 | sld_n = np.append(sld_n, _sld_n) |
---|
| 677 | sld_mx = np.append(sld_mx, _sld_mx) |
---|
| 678 | sld_my = np.append(sld_my, _sld_my) |
---|
| 679 | sld_mz = np.append(sld_mz, _sld_mz) |
---|
[51f14603] | 680 | try: |
---|
[e3f77d8b] | 681 | _vol_pix = float(toks[7]) |
---|
[9a5097c] | 682 | vol_pix = np.append(vol_pix, _vol_pix) |
---|
[51f14603] | 683 | except: |
---|
| 684 | vol_pix = None |
---|
| 685 | except: |
---|
| 686 | # Skip non-data lines |
---|
[c155a16] | 687 | logger.error(sys.exc_value) |
---|
[e3f77d8b] | 688 | output = MagSLD(pos_x, pos_y, pos_z, sld_n, |
---|
[51f14603] | 689 | sld_mx, sld_my, sld_mz) |
---|
| 690 | output.filename = os.path.basename(path) |
---|
| 691 | output.set_pix_type('pixel') |
---|
| 692 | output.set_pixel_symbols('pixel') |
---|
| 693 | if vol_pix != None: |
---|
| 694 | output.set_pixel_volumes(vol_pix) |
---|
| 695 | return output |
---|
| 696 | except: |
---|
[e3f77d8b] | 697 | raise RuntimeError, "%s is not a sld file" % path |
---|
| 698 | |
---|
[51f14603] | 699 | def write(self, path, data): |
---|
| 700 | """ |
---|
| 701 | Write sld file |
---|
[e3f77d8b] | 702 | :Param path: file path |
---|
[51f14603] | 703 | :Param data: MagSLD data object |
---|
| 704 | """ |
---|
| 705 | if path == None: |
---|
| 706 | raise ValueError, "Missing the file path." |
---|
| 707 | if data == None: |
---|
| 708 | raise ValueError, "Missing the data to save." |
---|
| 709 | x_val = data.pos_x |
---|
| 710 | y_val = data.pos_y |
---|
| 711 | z_val = data.pos_z |
---|
| 712 | vol_pix = data.vol_pix |
---|
| 713 | length = len(x_val) |
---|
| 714 | sld_n = data.sld_n |
---|
| 715 | if sld_n == None: |
---|
[9a5097c] | 716 | sld_n = np.zeros(length) |
---|
[51f14603] | 717 | sld_mx = data.sld_mx |
---|
| 718 | if sld_mx == None: |
---|
[9a5097c] | 719 | sld_mx = np.zeros(length) |
---|
| 720 | sld_my = np.zeros(length) |
---|
| 721 | sld_mz = np.zeros(length) |
---|
[51f14603] | 722 | else: |
---|
| 723 | sld_my = data.sld_my |
---|
| 724 | sld_mz = data.sld_mz |
---|
| 725 | out = open(path, 'w') |
---|
| 726 | # First Line: Column names |
---|
| 727 | out.write("X Y Z SLDN SLDMx SLDMy SLDMz VOLUMEpix") |
---|
| 728 | for ind in range(length): |
---|
[e3f77d8b] | 729 | out.write("\n%g %g %g %g %g %g %g %g" % \ |
---|
| 730 | (x_val[ind], y_val[ind], z_val[ind], sld_n[ind], |
---|
| 731 | sld_mx[ind], sld_my[ind], sld_mz[ind], vol_pix[ind])) |
---|
| 732 | out.close() |
---|
| 733 | |
---|
| 734 | |
---|
| 735 | class OMFData(object): |
---|
[51f14603] | 736 | """ |
---|
| 737 | OMF Data. |
---|
| 738 | """ |
---|
| 739 | _meshunit = "A" |
---|
| 740 | _valueunit = "A^(-2)" |
---|
| 741 | def __init__(self): |
---|
| 742 | """ |
---|
| 743 | Init for mag SLD |
---|
| 744 | """ |
---|
| 745 | self.filename = 'default' |
---|
| 746 | self.oommf = '' |
---|
| 747 | self.title = '' |
---|
| 748 | self.desc = '' |
---|
| 749 | self.meshtype = '' |
---|
| 750 | self.meshunit = self._meshunit |
---|
| 751 | self.valueunit = self._valueunit |
---|
| 752 | self.xbase = 0.0 |
---|
| 753 | self.ybase = 0.0 |
---|
| 754 | self.zbase = 0.0 |
---|
| 755 | self.xstepsize = 6.0 |
---|
| 756 | self.ystepsize = 6.0 |
---|
| 757 | self.zstepsize = 6.0 |
---|
| 758 | self.xnodes = 10.0 |
---|
| 759 | self.ynodes = 10.0 |
---|
| 760 | self.znodes = 10.0 |
---|
| 761 | self.xmin = 0.0 |
---|
| 762 | self.ymin = 0.0 |
---|
| 763 | self.zmin = 0.0 |
---|
| 764 | self.xmax = 60.0 |
---|
| 765 | self.ymax = 60.0 |
---|
| 766 | self.zmax = 60.0 |
---|
| 767 | self.mx = None |
---|
| 768 | self.my = None |
---|
| 769 | self.mz = None |
---|
| 770 | self.valuemultiplier = 1. |
---|
| 771 | self.valuerangeminmag = 0 |
---|
| 772 | self.valuerangemaxmag = 0 |
---|
[e3f77d8b] | 773 | |
---|
[51f14603] | 774 | def __str__(self): |
---|
| 775 | """ |
---|
| 776 | doc strings |
---|
| 777 | """ |
---|
[e3f77d8b] | 778 | _str = "Type: %s\n" % self.__class__.__name__ |
---|
[51f14603] | 779 | _str += "File: %s\n" % self.filename |
---|
| 780 | _str += "OOMMF: %s\n" % self.oommf |
---|
| 781 | _str += "Title: %s\n" % self.title |
---|
| 782 | _str += "Desc: %s\n" % self.desc |
---|
| 783 | _str += "meshtype: %s\n" % self.meshtype |
---|
| 784 | _str += "meshunit: %s\n" % str(self.meshunit) |
---|
| 785 | _str += "xbase: %s [%s]\n" % (str(self.xbase), self.meshunit) |
---|
| 786 | _str += "ybase: %s [%s]\n" % (str(self.ybase), self.meshunit) |
---|
| 787 | _str += "zbase: %s [%s]\n" % (str(self.zbase), self.meshunit) |
---|
[e3f77d8b] | 788 | _str += "xstepsize: %s [%s]\n" % (str(self.xstepsize), |
---|
[51f14603] | 789 | self.meshunit) |
---|
[e3f77d8b] | 790 | _str += "ystepsize: %s [%s]\n" % (str(self.ystepsize), |
---|
[51f14603] | 791 | self.meshunit) |
---|
[e3f77d8b] | 792 | _str += "zstepsize: %s [%s]\n" % (str(self.zstepsize), |
---|
[51f14603] | 793 | self.meshunit) |
---|
| 794 | _str += "xnodes: %s\n" % str(self.xnodes) |
---|
| 795 | _str += "ynodes: %s\n" % str(self.ynodes) |
---|
| 796 | _str += "znodes: %s\n" % str(self.znodes) |
---|
| 797 | _str += "xmin: %s [%s]\n" % (str(self.xmin), self.meshunit) |
---|
| 798 | _str += "ymin: %s [%s]\n" % (str(self.ymin), self.meshunit) |
---|
| 799 | _str += "zmin: %s [%s]\n" % (str(self.zmin), self.meshunit) |
---|
| 800 | _str += "xmax: %s [%s]\n" % (str(self.xmax), self.meshunit) |
---|
| 801 | _str += "ymax: %s [%s]\n" % (str(self.ymax), self.meshunit) |
---|
| 802 | _str += "zmax: %s [%s]\n" % (str(self.zmax), self.meshunit) |
---|
| 803 | _str += "valueunit: %s\n" % self.valueunit |
---|
| 804 | _str += "valuemultiplier: %s\n" % str(self.valuemultiplier) |
---|
[e3f77d8b] | 805 | _str += "ValueRangeMinMag:%s [%s]\n" % (str(self.valuerangeminmag), |
---|
| 806 | self.valueunit) |
---|
| 807 | _str += "ValueRangeMaxMag:%s [%s]\n" % (str(self.valuerangemaxmag), |
---|
| 808 | self.valueunit) |
---|
[51f14603] | 809 | return _str |
---|
[e3f77d8b] | 810 | |
---|
[51f14603] | 811 | def set_m(self, mx, my, mz): |
---|
| 812 | """ |
---|
| 813 | Set the Mx, My, Mz values |
---|
| 814 | """ |
---|
| 815 | self.mx = mx |
---|
| 816 | self.my = my |
---|
| 817 | self.mz = mz |
---|
[e3f77d8b] | 818 | |
---|
| 819 | class MagSLD(object): |
---|
[51f14603] | 820 | """ |
---|
| 821 | Magnetic SLD. |
---|
| 822 | """ |
---|
| 823 | pos_x = None |
---|
| 824 | pos_y = None |
---|
| 825 | pos_z = None |
---|
| 826 | sld_n = None |
---|
| 827 | sld_mx = None |
---|
| 828 | sld_my = None |
---|
| 829 | sld_mz = None |
---|
| 830 | # Units |
---|
| 831 | _pos_unit = 'A' |
---|
| 832 | _sld_unit = '1/A^(2)' |
---|
| 833 | _pix_type = 'pixel' |
---|
[e3f77d8b] | 834 | |
---|
| 835 | def __init__(self, pos_x, pos_y, pos_z, sld_n=None, |
---|
[51f14603] | 836 | sld_mx=None, sld_my=None, sld_mz=None, vol_pix=None): |
---|
| 837 | """ |
---|
| 838 | Init for mag SLD |
---|
| 839 | :params : All should be numpy 1D array |
---|
| 840 | """ |
---|
| 841 | self.is_data = True |
---|
| 842 | self.filename = '' |
---|
| 843 | self.xstepsize = 6.0 |
---|
| 844 | self.ystepsize = 6.0 |
---|
| 845 | self.zstepsize = 6.0 |
---|
| 846 | self.xnodes = 10.0 |
---|
| 847 | self.ynodes = 10.0 |
---|
| 848 | self.znodes = 10.0 |
---|
| 849 | self.has_stepsize = False |
---|
| 850 | self.has_conect = False |
---|
| 851 | self.pos_unit = self._pos_unit |
---|
| 852 | self.sld_unit = self._sld_unit |
---|
| 853 | self.pix_type = 'pixel' |
---|
| 854 | self.pos_x = pos_x |
---|
| 855 | self.pos_y = pos_y |
---|
| 856 | self.pos_z = pos_z |
---|
| 857 | self.sld_n = sld_n |
---|
| 858 | self.line_x = None |
---|
| 859 | self.line_y = None |
---|
| 860 | self.line_z = None |
---|
| 861 | self.sld_mx = sld_mx |
---|
| 862 | self.sld_my = sld_my |
---|
| 863 | self.sld_mz = sld_mz |
---|
| 864 | self.vol_pix = vol_pix |
---|
| 865 | self.sld_m = None |
---|
| 866 | self.sld_phi = None |
---|
| 867 | self.sld_theta = None |
---|
| 868 | self.pix_symbol = None |
---|
| 869 | if sld_mx != None and sld_my != None and sld_mz != None: |
---|
| 870 | self.set_sldms(sld_mx, sld_my, sld_mz) |
---|
| 871 | self.set_nodes() |
---|
[e3f77d8b] | 872 | |
---|
[51f14603] | 873 | def __str__(self): |
---|
| 874 | """ |
---|
| 875 | doc strings |
---|
| 876 | """ |
---|
[e3f77d8b] | 877 | _str = "Type: %s\n" % self.__class__.__name__ |
---|
[51f14603] | 878 | _str += "File: %s\n" % self.filename |
---|
| 879 | _str += "Axis_unit: %s\n" % self.pos_unit |
---|
| 880 | _str += "SLD_unit: %s\n" % self.sld_unit |
---|
| 881 | return _str |
---|
[e3f77d8b] | 882 | |
---|
[51f14603] | 883 | def set_pix_type(self, pix_type): |
---|
| 884 | """ |
---|
| 885 | Set pixel type |
---|
| 886 | :Param pix_type: string, 'pixel' or 'atom' |
---|
| 887 | """ |
---|
| 888 | self.pix_type = pix_type |
---|
[e3f77d8b] | 889 | |
---|
[51f14603] | 890 | def set_sldn(self, sld_n): |
---|
| 891 | """ |
---|
| 892 | Sets neutron SLD |
---|
| 893 | """ |
---|
| 894 | if sld_n.__class__.__name__ == 'float': |
---|
| 895 | if self.is_data: |
---|
[e3f77d8b] | 896 | # For data, put the value to only the pixels w non-zero M |
---|
[9a5097c] | 897 | is_nonzero = (np.fabs(self.sld_mx) + |
---|
| 898 | np.fabs(self.sld_my) + |
---|
| 899 | np.fabs(self.sld_mz)).nonzero() |
---|
| 900 | self.sld_n = np.zeros(len(self.pos_x)) |
---|
[51f14603] | 901 | if len(self.sld_n[is_nonzero]) > 0: |
---|
| 902 | self.sld_n[is_nonzero] = sld_n |
---|
| 903 | else: |
---|
| 904 | self.sld_n.fill(sld_n) |
---|
| 905 | else: |
---|
| 906 | # For non-data, put the value to all the pixels |
---|
[9a5097c] | 907 | self.sld_n = np.ones(len(self.pos_x)) * sld_n |
---|
[51f14603] | 908 | else: |
---|
| 909 | self.sld_n = sld_n |
---|
[e3f77d8b] | 910 | |
---|
[51f14603] | 911 | def set_sldms(self, sld_mx, sld_my, sld_mz): |
---|
[ac7be54] | 912 | r""" |
---|
| 913 | Sets (\|m\|, m_theta, m_phi) |
---|
[51f14603] | 914 | """ |
---|
| 915 | if sld_mx.__class__.__name__ == 'float': |
---|
[9a5097c] | 916 | self.sld_mx = np.ones(len(self.pos_x)) * sld_mx |
---|
[51f14603] | 917 | else: |
---|
| 918 | self.sld_mx = sld_mx |
---|
| 919 | if sld_my.__class__.__name__ == 'float': |
---|
[9a5097c] | 920 | self.sld_my = np.ones(len(self.pos_x)) * sld_my |
---|
[51f14603] | 921 | else: |
---|
| 922 | self.sld_my = sld_my |
---|
| 923 | if sld_mz.__class__.__name__ == 'float': |
---|
[9a5097c] | 924 | self.sld_mz = np.ones(len(self.pos_x)) * sld_mz |
---|
[51f14603] | 925 | else: |
---|
| 926 | self.sld_mz = sld_mz |
---|
| 927 | |
---|
[9a5097c] | 928 | sld_m = np.sqrt(sld_mx * sld_mx + sld_my * sld_my + \ |
---|
[e3f77d8b] | 929 | sld_mz * sld_mz) |
---|
[51f14603] | 930 | self.sld_m = sld_m |
---|
[e3f77d8b] | 931 | |
---|
| 932 | def set_pixel_symbols(self, symbol='pixel'): |
---|
[51f14603] | 933 | """ |
---|
| 934 | Set pixel |
---|
| 935 | :Params pixel: str; pixel or atomic symbol, or array of strings |
---|
| 936 | """ |
---|
| 937 | if self.sld_n == None: |
---|
| 938 | return |
---|
| 939 | if symbol.__class__.__name__ == 'str': |
---|
[9a5097c] | 940 | self.pix_symbol = np.repeat(symbol, len(self.sld_n)) |
---|
[51f14603] | 941 | else: |
---|
| 942 | self.pix_symbol = symbol |
---|
[e3f77d8b] | 943 | |
---|
| 944 | def set_pixel_volumes(self, vol): |
---|
[51f14603] | 945 | """ |
---|
| 946 | Set pixel volumes |
---|
| 947 | :Params pixel: str; pixel or atomic symbol, or array of strings |
---|
| 948 | """ |
---|
| 949 | if self.sld_n == None: |
---|
| 950 | return |
---|
| 951 | if vol.__class__.__name__ == 'ndarray': |
---|
| 952 | self.vol_pix = vol |
---|
| 953 | elif vol.__class__.__name__.count('float') > 0: |
---|
[9a5097c] | 954 | self.vol_pix = np.repeat(vol, len(self.sld_n)) |
---|
[51f14603] | 955 | else: |
---|
| 956 | self.vol_pix = None |
---|
| 957 | |
---|
| 958 | def get_sldn(self): |
---|
| 959 | """ |
---|
| 960 | Returns nuclear sld |
---|
| 961 | """ |
---|
| 962 | return self.sld_n |
---|
[e3f77d8b] | 963 | |
---|
[51f14603] | 964 | def set_nodes(self): |
---|
| 965 | """ |
---|
| 966 | Set xnodes, ynodes, and znodes |
---|
| 967 | """ |
---|
| 968 | self.set_stepsize() |
---|
| 969 | if self.pix_type == 'pixel': |
---|
| 970 | try: |
---|
| 971 | xdist = (max(self.pos_x) - min(self.pos_x)) / self.xstepsize |
---|
| 972 | ydist = (max(self.pos_y) - min(self.pos_y)) / self.ystepsize |
---|
| 973 | zdist = (max(self.pos_z) - min(self.pos_z)) / self.zstepsize |
---|
| 974 | self.xnodes = int(xdist) + 1 |
---|
| 975 | self.ynodes = int(ydist) + 1 |
---|
| 976 | self.znodes = int(zdist) + 1 |
---|
| 977 | except: |
---|
| 978 | self.xnodes = None |
---|
| 979 | self.ynodes = None |
---|
| 980 | self.znodes = None |
---|
| 981 | else: |
---|
| 982 | self.xnodes = None |
---|
| 983 | self.ynodes = None |
---|
| 984 | self.znodes = None |
---|
[e3f77d8b] | 985 | |
---|
[51f14603] | 986 | def set_stepsize(self): |
---|
| 987 | """ |
---|
| 988 | Set xtepsize, ystepsize, and zstepsize |
---|
| 989 | """ |
---|
| 990 | if self.pix_type == 'pixel': |
---|
| 991 | try: |
---|
| 992 | xpos_pre = self.pos_x[0] |
---|
| 993 | ypos_pre = self.pos_y[0] |
---|
| 994 | zpos_pre = self.pos_z[0] |
---|
| 995 | for x_pos in self.pos_x: |
---|
| 996 | if xpos_pre != x_pos: |
---|
[9a5097c] | 997 | self.xstepsize = np.fabs(x_pos - xpos_pre) |
---|
[51f14603] | 998 | break |
---|
| 999 | for y_pos in self.pos_y: |
---|
| 1000 | if ypos_pre != y_pos: |
---|
[9a5097c] | 1001 | self.ystepsize = np.fabs(y_pos - ypos_pre) |
---|
[51f14603] | 1002 | break |
---|
| 1003 | for z_pos in self.pos_z: |
---|
| 1004 | if zpos_pre != z_pos: |
---|
[9a5097c] | 1005 | self.zstepsize = np.fabs(z_pos - zpos_pre) |
---|
[51f14603] | 1006 | break |
---|
| 1007 | #default pix volume |
---|
[9a5097c] | 1008 | self.vol_pix = np.ones(len(self.pos_x)) |
---|
[51f14603] | 1009 | vol = self.xstepsize * self.ystepsize * self.zstepsize |
---|
| 1010 | self.set_pixel_volumes(vol) |
---|
| 1011 | self.has_stepsize = True |
---|
| 1012 | except: |
---|
| 1013 | self.xstepsize = None |
---|
| 1014 | self.ystepsize = None |
---|
| 1015 | self.zstepsize = None |
---|
| 1016 | self.vol_pix = None |
---|
| 1017 | self.has_stepsize = False |
---|
| 1018 | else: |
---|
| 1019 | self.xstepsize = None |
---|
| 1020 | self.ystepsize = None |
---|
| 1021 | self.zstepsize = None |
---|
| 1022 | self.has_stepsize = True |
---|
| 1023 | return self.xstepsize, self.ystepsize, self.zstepsize |
---|
| 1024 | |
---|
| 1025 | def set_conect_lines(self, line_x, line_y, line_z): |
---|
| 1026 | """ |
---|
| 1027 | Set bonding line data if taken from pdb |
---|
| 1028 | """ |
---|
| 1029 | if line_x.__class__.__name__ != 'list' or len(line_x) < 1: |
---|
| 1030 | return |
---|
| 1031 | if line_y.__class__.__name__ != 'list' or len(line_y) < 1: |
---|
| 1032 | return |
---|
| 1033 | if line_z.__class__.__name__ != 'list' or len(line_z) < 1: |
---|
| 1034 | return |
---|
| 1035 | self.has_conect = True |
---|
[e3f77d8b] | 1036 | self.line_x = line_x |
---|
| 1037 | self.line_y = line_y |
---|
[51f14603] | 1038 | self.line_z = line_z |
---|
| 1039 | |
---|
| 1040 | def test_load(): |
---|
[b6627d9] | 1041 | """ |
---|
| 1042 | Test code |
---|
| 1043 | """ |
---|
[06aaa75d] | 1044 | from mpl_toolkits.mplot3d import Axes3D |
---|
[e3f77d8b] | 1045 | current_dir = os.path.abspath(os.path.curdir) |
---|
| 1046 | print current_dir |
---|
[51f14603] | 1047 | for i in range(6): |
---|
[e3f77d8b] | 1048 | current_dir, _ = os.path.split(current_dir) |
---|
| 1049 | tfile = os.path.join(current_dir, "test", "CoreXY_ShellZ.txt") |
---|
| 1050 | ofile = os.path.join(current_dir, "test", "A_Raw_Example-1.omf") |
---|
[51f14603] | 1051 | if os.path.isfile(tfile): |
---|
| 1052 | tfpath = tfile |
---|
| 1053 | ofpath = ofile |
---|
| 1054 | break |
---|
| 1055 | reader = SLDReader() |
---|
| 1056 | oreader = OMFReader() |
---|
| 1057 | output = reader.read(tfpath) |
---|
| 1058 | ooutput = oreader.read(ofpath) |
---|
| 1059 | foutput = OMF2SLD() |
---|
| 1060 | foutput.set_data(ooutput) |
---|
| 1061 | |
---|
| 1062 | import matplotlib.pyplot as plt |
---|
| 1063 | fig = plt.figure() |
---|
[06aaa75d] | 1064 | ax = Axes3D(fig) |
---|
[e3f77d8b] | 1065 | ax.plot(output.pos_x, output.pos_y, output.pos_z, '.', c="g", |
---|
| 1066 | alpha=0.7, markeredgecolor='gray', rasterized=True) |
---|
[51f14603] | 1067 | gap = 7 |
---|
| 1068 | max_mx = max(output.sld_mx) |
---|
| 1069 | max_my = max(output.sld_my) |
---|
| 1070 | max_mz = max(output.sld_mz) |
---|
[e3f77d8b] | 1071 | max_m = max(max_mx, max_my, max_mz) |
---|
[51f14603] | 1072 | x2 = output.pos_x+output.sld_mx/max_m * gap |
---|
| 1073 | y2 = output.pos_y+output.sld_my/max_m * gap |
---|
| 1074 | z2 = output.pos_z+output.sld_mz/max_m * gap |
---|
[9a5097c] | 1075 | x_arrow = np.column_stack((output.pos_x, x2)) |
---|
| 1076 | y_arrow = np.column_stack((output.pos_y, y2)) |
---|
| 1077 | z_arrow = np.column_stack((output.pos_z, z2)) |
---|
[51f14603] | 1078 | unit_x2 = output.sld_mx / max_m |
---|
| 1079 | unit_y2 = output.sld_my / max_m |
---|
| 1080 | unit_z2 = output.sld_mz / max_m |
---|
[9a5097c] | 1081 | color_x = np.fabs(unit_x2 * 0.8) |
---|
| 1082 | color_y = np.fabs(unit_y2 * 0.8) |
---|
| 1083 | color_z = np.fabs(unit_z2 * 0.8) |
---|
| 1084 | colors = np.column_stack((color_x, color_y, color_z)) |
---|
[51f14603] | 1085 | plt.show() |
---|
[b6627d9] | 1086 | |
---|
[51f14603] | 1087 | def test(): |
---|
[b6627d9] | 1088 | """ |
---|
| 1089 | Test code |
---|
| 1090 | """ |
---|
[e3f77d8b] | 1091 | current_dir = os.path.abspath(os.path.curdir) |
---|
[51f14603] | 1092 | for i in range(3): |
---|
[e3f77d8b] | 1093 | current_dir, _ = os.path.split(current_dir) |
---|
| 1094 | ofile = os.path.join(current_dir, "test", "A_Raw_Example-1.omf") |
---|
[51f14603] | 1095 | if os.path.isfile(ofile): |
---|
| 1096 | ofpath = ofile |
---|
| 1097 | break |
---|
| 1098 | oreader = OMFReader() |
---|
| 1099 | ooutput = oreader.read(ofpath) |
---|
[e3f77d8b] | 1100 | foutput = OMF2SLD() |
---|
| 1101 | foutput.set_data(ooutput) |
---|
| 1102 | writer = SLDReader() |
---|
| 1103 | writer.write(os.path.join(os.path.dirname(ofpath), "out.txt"), |
---|
[51f14603] | 1104 | foutput.output) |
---|
| 1105 | model = GenSAS() |
---|
[e3f77d8b] | 1106 | model.set_sld_data(foutput.output) |
---|
[9a5097c] | 1107 | x = np.arange(1000)/10000. + 1e-5 |
---|
| 1108 | y = np.arange(1000)/10000. + 1e-5 |
---|
| 1109 | i = np.zeros(1000) |
---|
[e3f77d8b] | 1110 | model.runXY([x, y, i]) |
---|
| 1111 | |
---|
| 1112 | if __name__ == "__main__": |
---|
[51f14603] | 1113 | test() |
---|
| 1114 | test_load() |
---|