1 | from __future__ import print_function |
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2 | |
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3 | import sys, os, math, re |
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4 | import numpy as np |
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5 | import matplotlib |
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6 | matplotlib.use('Agg') |
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7 | import matplotlib.pyplot as plt |
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8 | sys.path.insert(0, os.path.abspath('..')) |
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9 | import sasmodels |
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10 | from sasmodels import generate, core |
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11 | from sasmodels.direct_model import DirectModel, call_profile |
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12 | from sasmodels.data import empty_data1D, empty_data2D |
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13 | |
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14 | try: |
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15 | from typing import Dict, Any |
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16 | except ImportError: |
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17 | pass |
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18 | else: |
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19 | from matplotlib.axes import Axes |
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20 | from sasmodels.kernel import KernelModel |
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21 | from sasmodels.modelinfo import ModelInfo |
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22 | |
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23 | |
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24 | def plot_1d(model, opts, ax): |
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25 | # type: (KernelModel, Dict[str, Any], Axes) -> None |
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26 | """ |
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27 | Create a 1-D image. |
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28 | """ |
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29 | q_min, q_max, nq = opts['q_min'], opts['q_max'], opts['nq'] |
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30 | q_min = math.log10(q_min) |
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31 | q_max = math.log10(q_max) |
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32 | q = np.logspace(q_min, q_max, nq) |
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33 | data = empty_data1D(q) |
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34 | calculator = DirectModel(data, model) |
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35 | Iq1D = calculator() |
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36 | |
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37 | ax.plot(q, Iq1D, color='blue', lw=2, label=model.info.name) |
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38 | ax.set_xlabel(r'$Q \/(\AA^{-1})$') |
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39 | ax.set_ylabel(r'$I(Q) \/(\mathrm{cm}^{-1})$') |
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40 | ax.set_xscale(opts['xscale']) |
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41 | ax.set_yscale(opts['yscale']) |
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42 | #ax.legend(loc='best') |
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43 | |
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44 | def plot_2d(model, opts, ax): |
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45 | # type: (KernelModel, Dict[str, Any], Axes) -> None |
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46 | """ |
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47 | Create a 2-D image. |
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48 | """ |
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49 | qx_max, nq2d = opts['qx_max'], opts['nq2d'] |
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50 | q = np.linspace(-qx_max, qx_max, nq2d) # type: np.ndarray |
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51 | data2d = empty_data2D(q, resolution=0.0) |
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52 | calculator = DirectModel(data2d, model) |
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53 | Iq2D = calculator() #background=0) |
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54 | Iq2D = Iq2D.reshape(nq2d, nq2d) |
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55 | if opts['zscale'] == 'log': |
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56 | Iq2D = np.log(np.clip(Iq2D, opts['vmin'], np.inf)) |
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57 | ax.imshow(Iq2D, interpolation='nearest', aspect=1, origin='lower', |
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58 | extent=[-qx_max, qx_max, -qx_max, qx_max], cmap=opts['colormap']) |
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59 | ax.set_xlabel(r'$Q_x \/(\AA^{-1})$') |
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60 | ax.set_ylabel(r'$Q_y \/(\AA^{-1})$') |
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61 | |
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62 | def plot_profile_inset(model_info, ax): |
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63 | p = ax.get_position() |
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64 | width, height = 0.4*(p.x1-p.x0), 0.4*(p.y1-p.y0) |
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65 | left, bottom = p.x1-width, p.y1-height |
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66 | inset = plt.gcf().add_axes([left, bottom, width, height]) |
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67 | x, y, labels = call_profile(model_info) |
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68 | inset.plot(x, y, '-') |
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69 | inset.locator_params(nbins=4) |
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70 | #inset.set_xlabel(labels[0]) |
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71 | #inset.set_ylabel(labels[1]) |
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72 | inset.text(0.99, 0.99, "profile", |
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73 | horizontalalignment="right", |
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74 | verticalalignment="top", |
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75 | transform=inset.transAxes) |
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76 | |
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77 | def figfile(model_info): |
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78 | # type: (ModelInfo) -> str |
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79 | return model_info.id + '_autogenfig.png' |
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80 | |
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81 | def make_figure(model_info, opts): |
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82 | # type: (ModelInfo, Dict[str, Any]) -> None |
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83 | """ |
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84 | Generate the figure file to include in the docs. |
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85 | """ |
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86 | model = core.build_model(model_info) |
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87 | |
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88 | fig_height = 3.0 # in |
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89 | fig_left = 0.6 # in |
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90 | fig_right = 0.5 # in |
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91 | fig_top = 0.6*0.25 # in |
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92 | fig_bottom = 0.6*0.75 |
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93 | if model_info.parameters.has_2d: |
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94 | plot_height = fig_height - (fig_top+fig_bottom) |
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95 | plot_width = plot_height |
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96 | fig_width = 2*(plot_width + fig_left + fig_right) |
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97 | aspect = (fig_width, fig_height) |
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98 | ratio = aspect[0]/aspect[1] |
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99 | ax_left = fig_left/fig_width |
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100 | ax_bottom = fig_bottom/fig_height |
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101 | ax_height = plot_height/fig_height |
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102 | ax_width = ax_height/ratio # square axes |
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103 | fig = plt.figure(figsize=aspect) |
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104 | ax2d = fig.add_axes([0.5+ax_left, ax_bottom, ax_width, ax_height]) |
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105 | plot_2d(model, opts, ax2d) |
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106 | ax1d = fig.add_axes([ax_left, ax_bottom, ax_width, ax_height]) |
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107 | plot_1d(model, opts, ax1d) |
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108 | #ax.set_aspect('square') |
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109 | else: |
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110 | plot_height = fig_height - (fig_top+fig_bottom) |
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111 | plot_width = (1+np.sqrt(5))/2*fig_height |
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112 | fig_width = plot_width + fig_left + fig_right |
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113 | ax_left = fig_left/fig_width |
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114 | ax_bottom = fig_bottom/fig_height |
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115 | ax_width = plot_width/fig_width |
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116 | ax_height = plot_height/fig_height |
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117 | aspect = (fig_width, fig_height) |
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118 | fig = plt.figure(figsize=aspect) |
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119 | ax1d = fig.add_axes([ax_left, ax_bottom, ax_width, ax_height]) |
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120 | plot_1d(model, opts, ax1d) |
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121 | |
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122 | if model_info.profile: |
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123 | plot_profile_inset(model_info, ax1d) |
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124 | |
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125 | # Save image in model/img |
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126 | path = os.path.join('model', 'img', figfile(model_info)) |
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127 | plt.savefig(path, bbox_inches='tight') |
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128 | #print("figure saved in",path) |
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129 | |
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130 | def copy_if_newer(src, dst): |
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131 | from os.path import dirname, exists, getmtime |
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132 | import shutil |
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133 | if not exists(dst): |
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134 | path = dirname(dst) |
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135 | if not exists(path): |
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136 | os.makedirs(path) |
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137 | shutil.copy2(src, dst) |
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138 | elif getmtime(src) > getmtime(dst): |
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139 | shutil.copy2(src, dst) |
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140 | |
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141 | def link_sources(model_info): |
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142 | from os.path import basename, dirname, realpath, join as joinpath |
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143 | |
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144 | # List source files in reverse order of dependency. |
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145 | model_file = basename(model_info.filename) |
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146 | sources = list(reversed(model_info.source + [model_file])) |
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147 | |
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148 | # Copy files to src dir under models directory. Need to do this |
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149 | # because sphinx can't link to an absolute path. |
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150 | root = dirname(dirname(realpath(__file__))) |
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151 | src = joinpath(root, "sasmodels", "models") |
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152 | dst = joinpath(root, "doc", "model", "src") |
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153 | for path in sources: |
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154 | copy_if_newer(joinpath(src, path), joinpath(dst, path)) |
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155 | |
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156 | # Link to local copy of the files |
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157 | downloads = [":download:`%s <src/%s>`"%(path, path) for path in sources] |
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158 | |
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159 | # Could do syntax highlighting on the model files by creating a rst file |
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160 | # beside each source file named containing source file with |
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161 | # |
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162 | # src/path.rst: |
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163 | # |
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164 | # .. {{ path.replace('/','_') }}: |
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165 | # |
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166 | # .. literalinclude:: {{ src/path }} |
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167 | # :language: {{ "python" if path.endswith('.py') else "c" }} |
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168 | # :linenos: |
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169 | # |
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170 | # and link to it using |
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171 | # |
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172 | # colors = [":ref:`%s`"%(path.replace('/','_')) for path in sources] |
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173 | # |
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174 | # Probably need to dump all the rst files into an index.rst to build them. |
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175 | |
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176 | # Link to github repo (either the tagged sasmodels version or master) |
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177 | url = "https://github.com/SasView/sasmodels/blob/v%s"%sasmodels.__version__ |
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178 | #url = "https://github.com/SasView/sasmodels/blob/master"%sasmodels.__version__ |
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179 | links = ["`%s <%s/sasmodels/models/%s>`_"%(path, url, path) for path in sources] |
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180 | |
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181 | sep = "\n$\\ \\star\\ $ " # bullet |
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182 | body = "\n**Source**\n" |
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183 | #body += "\n" + sep.join(links) + "\n\n" |
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184 | body += "\n" + sep.join(downloads) + "\n\n" |
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185 | return body |
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186 | |
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187 | def gen_docs(model_info): |
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188 | # type: (ModelInfo) -> None |
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189 | """ |
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190 | Generate the doc string with the figure inserted before the references. |
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191 | """ |
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192 | |
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193 | # Load the doc string from the module definition file and store it in rst |
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194 | docstr = generate.make_doc(model_info) |
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195 | |
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196 | # Auto caption for figure |
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197 | captionstr = '\n' |
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198 | captionstr += '.. figure:: img/' + figfile(model_info) + '\n' |
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199 | captionstr += '\n' |
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200 | if model_info.parameters.has_2d: |
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201 | captionstr += ' 1D and 2D plots corresponding to the default parameters of the model.\n' |
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202 | else: |
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203 | captionstr += ' 1D plot corresponding to the default parameters of the model.\n' |
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204 | captionstr += '\n' |
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205 | |
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206 | # Add figure reference and caption to documentation (at end, before References) |
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207 | pattern = '\*\*REFERENCE' |
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208 | match = re.search(pattern, docstr.upper()) |
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209 | |
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210 | sources = link_sources(model_info) |
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211 | |
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212 | insertion = captionstr + sources |
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213 | |
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214 | if match: |
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215 | docstr1 = docstr[:match.start()] |
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216 | docstr2 = docstr[match.start():] |
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217 | docstr = docstr1 + insertion + docstr2 |
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218 | else: |
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219 | print('------------------------------------------------------------------') |
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220 | print('References NOT FOUND for model: ', model_info.id) |
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221 | print('------------------------------------------------------------------') |
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222 | docstr += insertion |
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223 | |
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224 | open(sys.argv[2], 'w').write(docstr) |
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225 | |
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226 | def process_model(path): |
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227 | # type: (str) -> None |
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228 | """ |
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229 | Generate doc file and image file for the given model definition file. |
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230 | """ |
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231 | |
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232 | # Load the model file |
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233 | model_name = os.path.basename(path)[:-3] |
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234 | model_info = core.load_model_info(model_name) |
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235 | |
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236 | # Plotting ranges and options |
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237 | opts = { |
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238 | 'xscale' : 'log', |
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239 | 'yscale' : 'log' if not model_info.structure_factor else 'linear', |
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240 | 'zscale' : 'log' if not model_info.structure_factor else 'linear', |
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241 | 'q_min' : 0.001, |
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242 | 'q_max' : 1.0, |
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243 | 'nq' : 1000, |
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244 | 'nq2d' : 1000, |
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245 | 'vmin' : 1e-3, # floor for the 2D data results |
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246 | 'qx_max' : 0.5, |
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247 | #'colormap' : 'gist_ncar', |
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248 | 'colormap' : 'nipy_spectral', |
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249 | #'colormap' : 'jet', |
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250 | } |
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251 | |
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252 | # Generate the RST file and the figure. Order doesn't matter. |
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253 | gen_docs(model_info) |
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254 | make_figure(model_info, opts) |
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255 | |
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256 | if __name__ == "__main__": |
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257 | process_model(sys.argv[1]) |
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