reflectometry.model1d.adaptor.reflModel

22 """ 23 Model class for Refl. 24 """ 25

26 - def __init__(self, 27 name, 28 magnetic=False 29 ):

30 """ 31 Constructor. A model must have a name. 32 """ 33 FitModel.__init__(self, REFL_PM_TAG, name) 34 self.magnetic = magnetic

35 36

37 - def getClassName(self):

38 """ 39 Return the full class name 40 """ 41 return 'reflModel.ReflModel'

42 43

44 - def clear(self):

45 """ 46 clear the contents of the model. 47 """ 48 self._pmNames = [] 49 self.setData([])

50 51

52 - def getParameters(self):

53 """ 54 Return a list of strings representing the fitting parameter names. 55 The user class override this function. 56 """ 57 pms = [] 58 for name in self._pmNames: 59 pm = getattr(self, name) 60 pms.extend(pm.getParameters()) 61 return pms

62 63

64 - def getLayers(self):

65 """ 66 Return a list of parameters for the model. 67 """ 68 return [getattr(self, name) for name in self._pmNames ]

69 70

71 - def getLayer(self, pname):

72 """ 73 Return a list of parameters for the model. 74 """ 75 return getattr(self, pname)

76 77

78 - def addLayer(self, pmName):

79 """ 80 Add a fitting parameter to the model. 81 pmName is the parameter's name that should not include the model name. 82 """ 83 pm = ReflParameterSet(pmName) 84 setattr(self, pmName, pm) 85 self._pmNames.append(pmName)

86 87 88

89 - def layer(self, 90 name, 91 depth =100.0, 92 sigma =0.0, 93 rho =1.0, 94 mu =0.0, 95 rho_m =0.0, 96 theta_m=0.0 97 ):

98 if self.magnetic: pm = ReflMagParameterSet( name ) 99 else: pm = ReflParameterSet( name ) 100 setattr(self, name, pm) 101 self._pmNames.append( name ) 102 103 pm.depth = depth 104 pm.rough = sigma 105 pm.rho = rho 106 pm.mu = mu 107 if self.magnetic: 108 pm.rho_m = rho_m 109 pm.theta_m = theta_m

110 111

112 - def incident(self,name, depth=100.0, sigma=0.0, rho=1.0, mu=0.0, 113 rho_m=0.0, theta_m=0.0):

114 self.layer(name,depth, sigma,rho,mu,rho_m,theta_m)

115 116

117 - def substrate(self, name, depth=100.0, sigma=0.0, rho=1.0, mu=0.0, 118 rho_m=0.0, theta_m=0.0):

119 self.layer(name,depth, sigma,rho,mu,rho_m,theta_m)

120 121

122 - def interface(self, rough=5.0):

123 index = len(self._pmNames)-1 124 pm=self.getLayer(self._pmNames[index]) 125 pm.rough=rough

126 127

128 - def removeLayer(self, pmName):

129 """ 130 remove a parameter by its name. 131 """ 132 self._pmNames.remove(pmName) 133 delattr(self, pmName)

134 135

136 - def __call__(self):

137 """ 138 Return the result for the simulation. 139 """ 140 xdata = self.getData()[0] 141 R = CalcReflectivity( xdata, self.getLayers() ) 142 143 return R

144 145

146 - def getResidual(self):

147 """ 148 Return a vector to calculate norm2. It is required by 149 leastsq() method to calculate the error bar of parameters. 150 """ 151 if len(self.getData()) == 3: # Q R dR 152 dy = (self() - self.getData()[1])/self.getData()[2] 153 154 elif len(self.getData()) == 4: #Q, dQ, R, dQ 155 dy = (self() - self.getData()[2])/self.getData()[3] 156 157 elif len(self.getData()) == 5: #Q, dQ, R, dQ, Wavelength 158 dy = (self() - self.getData()[2])/self.getData()[3] 159 else: 160 dy = None 161 162 return dy

163 164

165 - def getChisq(self):

166 """ 167 Return the chisq value for the optimization. 168 This provides the default implementation, which is 169 || residual ||^2. 170 """ 171 dy = self.getResidual() 172 return numpy.dot(dy, dy)/len(self.getData()[0])

173 174

175 - def fromPyFile(self, fname):

176 """ 177 Rebuild the object from an python script file 178 """ 179 fin = open( fname, 'r') 180 pyTxts = fin.read() 181 cmds = self._parsePyTexts(pyTxts) 182 for cmd in cmds: 183 exec cmd

184 185

186 - def toPyFile(self, fname):

187 """ 188 Save the object in a file in python format. 189 fname: a file name or a file handler. 190 Return true when successes. 191 """ 192 fout = None 193 try: 194 fout = open(fname, 'w') 195 fout.write(str0) 196 except: 197 pass 198 199 if fout is not None: fd.close()

200 201

202 - def _parsePyTexts(self, pyTxts):

203 """ 204 restore information about Refl model. 205 """ 206 s=pyTxts.strip().split('\n') 207 for i in xrange(len(s)): 208 line=s[i] 209 cmd=line.strip().split('(')[0].strip() 210 if cmd in ('incident','layer','interface', 'substrate'): 211 s[i] = 'self.'+ line 212 return s

213 214

215 - def _parseChildren(self, xmlNode):

216 """ 217 restore information about Refl model. 218 """ 219 for node in xmlNode.childNodes: 220 if node.nodeType == dom.Node.ELEMENT_NODE: 221 if node.nodeName == REFL_PS_TAG: 222 name = node.getAttribute(NAME_TAG) 223 pm = ReflParameterSet(name) 224 pm.parse(node) 225 self._pmNames.append(name) 226 setattr(self, name, pm) 227 228 elif node.nodeName == DATA_TAG: 229 self.setData(dataFromXml(node)) 230 else: 231 pass

Source Code for Module reflectometry.model1d.adaptor.reflModel