def setUp(self):
shutil.copytree(os.path.join('..', 'examples', 'noise'),
os.path.join('..', 'examples', '__tmp_noise'))
dpkgRoot = os.path.join('..', 'examples', 'noise')
dpkg = json.load(open(os.path.join(dpkgRoot, 'package.json')))
self.m_noise = Ccoder(dpkgRoot, copy.deepcopy(dpkg))
m_diff = copy.deepcopy(dpkg)
del m_diff['model']['reactions'][2]['white_noise']
del m_diff['model']['reactions'][3]['white_noise']
m_diff['model']['sde'] = {
'drift': [{
'name': 'r0_paris',
'f': 0.0,
'transformation': 'log(r0_paris)'
}, {
'name': 'r0_nyc',
'f': 0.0,
'transformation': 'log(r0_nyc)'
}],
'dispertion': [['vol', 0], [0, 'vol']]
}
self.m_diff = Ccoder(dpkgRoot, m_diff)
m_noise2 = copy.deepcopy(dpkg)
del m_noise2['model']['reactions'][2]['white_noise']
del m_noise2['model']['reactions'][3]['white_noise']
m_noise2['model']['reactions'][0]['white_noise'] = {
'name': 'noise_SI',
'sd': 'sto'
}
m_noise2['model']['reactions'][1]['white_noise'] = {
'name': 'noise_SI2',
'sd': 'sto'
}
self.m_noise2 = Ccoder(dpkgRoot, m_noise2)
m_noise3 = copy.deepcopy(dpkg)
del m_noise3['model']['reactions'][2]['white_noise']
del m_noise3['model']['reactions'][3]['white_noise']
m_noise3['model']['reactions'][4]['white_noise'] = {
'name': 'noise_SI',
'sd': 'sto'
}
m_noise3['model']['reactions'][5]['white_noise'] = {
'name': 'noise_SI2',
'sd': 'sto'
}
self.m_noise3 = Ccoder(dpkgRoot, m_noise3)
m_noise4 = copy.deepcopy(dpkg)
del m_noise4['model']['reactions'][2]['white_noise']
del m_noise4['model']['reactions'][3]['white_noise']
m_noise4['model']['reactions'][8]['white_noise'] = {
'name': 'noise_SI',
'sd': 'sto'
}
m_noise4['model']['reactions'][9]['white_noise'] = {
'name': 'noise_SI2',
'sd': 'sto'
}
self.m_noise4 = Ccoder(dpkgRoot, m_noise4)
m_noise5 = copy.deepcopy(dpkg)
del m_noise5['model']['reactions'][2]['white_noise']
del m_noise5['model']['reactions'][3]['white_noise']
m_noise5['model']['reactions'][10]['white_noise'] = {
'name': 'noise_SI',
'sd': 'sto'
}
m_noise5['model']['reactions'][11]['white_noise'] = {
'name': 'noise_SI2',
'sd': 'sto'
}
self.m_noise5 = Ccoder(dpkgRoot, m_noise5)
m_noise6 = copy.deepcopy(dpkg)
m_noise6['model']['reactions'][4]['white_noise'] = {
'name': 'noise_SI',
'sd': 'sto'
}
m_noise6['model']['reactions'][5]['white_noise'] = {
'name': 'noise_SI2',
'sd': 'sto'
}
self.m_noise6 = Ccoder(dpkgRoot, m_noise6)
m_noise7 = copy.deepcopy(dpkg)
m_noise7['model']['reactions'][4]['white_noise'] = {
'name': 'noise_SI23',
'sd': 'sto'
}
m_noise7['model']['reactions'][5]['white_noise'] = {
'name': 'noise_SI24',
'sd': 'sto'
}
self.m_noise7 = Ccoder(dpkgRoot, m_noise7)
m_diff2 = copy.deepcopy(dpkg)
del m_diff2['model']['reactions'][2]['white_noise']
del m_diff2['model']['reactions'][3]['white_noise']
m_diff2['model']['sde'] = copy.deepcopy(m_diff['model']['sde'])
m_diff2['model']['reactions'].append({
'from': 'R_paris',
'to': 'I_paris',
'rate': 'correct_rate(v)',
'description': 'testing'
})
m_diff2['model']['reactions'].append({
'from': 'R_nyc',
'to': 'I_nyc',
'rate': 'correct_rate(v)',
'description': 'testing'
})
self.m_diff2 = Ccoder(dpkgRoot, m_diff2)
