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See the NOTICE file distributed with<a name="line.3"></a> -<span class="sourceLineNo">004</span> * this work for additional information regarding copyright ownership.<a name="line.4"></a> -<span class="sourceLineNo">005</span> * The ASF licenses this file to You under the Apache License, Version 2.0<a name="line.5"></a> -<span class="sourceLineNo">006</span> * (the "License"); you may not use this file except in compliance with<a name="line.6"></a> -<span class="sourceLineNo">007</span> * the License. You may obtain a copy of the License at<a name="line.7"></a> -<span class="sourceLineNo">008</span> *<a name="line.8"></a> -<span class="sourceLineNo">009</span> * http://www.apache.org/licenses/LICENSE-2.0<a name="line.9"></a> -<span class="sourceLineNo">010</span> *<a name="line.10"></a> -<span class="sourceLineNo">011</span> * Unless required by applicable law or agreed to in writing, software<a name="line.11"></a> -<span class="sourceLineNo">012</span> * distributed under the License is distributed on an "AS IS" BASIS,<a name="line.12"></a> -<span class="sourceLineNo">013</span> * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.<a name="line.13"></a> -<span class="sourceLineNo">014</span> * See the License for the specific language governing permissions and<a name="line.14"></a> -<span class="sourceLineNo">015</span> * limitations under the License.<a name="line.15"></a> -<span class="sourceLineNo">016</span> */<a name="line.16"></a> -<span class="sourceLineNo">017</span><a name="line.17"></a> -<span class="sourceLineNo">018</span>package org.apache.commons.math3.optimization.general;<a name="line.18"></a> -<span class="sourceLineNo">019</span><a name="line.19"></a> -<span class="sourceLineNo">020</span>import org.apache.commons.math3.analysis.DifferentiableMultivariateVectorFunction;<a name="line.20"></a> -<span class="sourceLineNo">021</span>import org.apache.commons.math3.analysis.FunctionUtils;<a name="line.21"></a> -<span class="sourceLineNo">022</span>import org.apache.commons.math3.analysis.differentiation.DerivativeStructure;<a name="line.22"></a> -<span class="sourceLineNo">023</span>import org.apache.commons.math3.analysis.differentiation.MultivariateDifferentiableVectorFunction;<a name="line.23"></a> -<span class="sourceLineNo">024</span>import org.apache.commons.math3.exception.DimensionMismatchException;<a name="line.24"></a> -<span class="sourceLineNo">025</span>import org.apache.commons.math3.exception.NumberIsTooSmallException;<a name="line.25"></a> -<span class="sourceLineNo">026</span>import org.apache.commons.math3.exception.util.LocalizedFormats;<a name="line.26"></a> -<span class="sourceLineNo">027</span>import org.apache.commons.math3.linear.ArrayRealVector;<a name="line.27"></a> -<span class="sourceLineNo">028</span>import org.apache.commons.math3.linear.RealMatrix;<a name="line.28"></a> -<span class="sourceLineNo">029</span>import org.apache.commons.math3.linear.DiagonalMatrix;<a name="line.29"></a> -<span class="sourceLineNo">030</span>import org.apache.commons.math3.linear.DecompositionSolver;<a name="line.30"></a> -<span class="sourceLineNo">031</span>import org.apache.commons.math3.linear.MatrixUtils;<a name="line.31"></a> -<span class="sourceLineNo">032</span>import org.apache.commons.math3.linear.QRDecomposition;<a name="line.32"></a> -<span class="sourceLineNo">033</span>import org.apache.commons.math3.linear.EigenDecomposition;<a name="line.33"></a> -<span class="sourceLineNo">034</span>import org.apache.commons.math3.optimization.OptimizationData;<a name="line.34"></a> -<span class="sourceLineNo">035</span>import org.apache.commons.math3.optimization.InitialGuess;<a name="line.35"></a> -<span class="sourceLineNo">036</span>import org.apache.commons.math3.optimization.Target;<a name="line.36"></a> -<span class="sourceLineNo">037</span>import org.apache.commons.math3.optimization.Weight;<a name="line.37"></a> -<span class="sourceLineNo">038</span>import org.apache.commons.math3.optimization.ConvergenceChecker;<a name="line.38"></a> -<span class="sourceLineNo">039</span>import org.apache.commons.math3.optimization.DifferentiableMultivariateVectorOptimizer;<a name="line.39"></a> -<span class="sourceLineNo">040</span>import org.apache.commons.math3.optimization.PointVectorValuePair;<a name="line.40"></a> -<span class="sourceLineNo">041</span>import org.apache.commons.math3.optimization.direct.BaseAbstractMultivariateVectorOptimizer;<a name="line.41"></a> -<span class="sourceLineNo">042</span>import org.apache.commons.math3.util.FastMath;<a name="line.42"></a> -<span class="sourceLineNo">043</span><a name="line.43"></a> -<span class="sourceLineNo">044</span>/**<a name="line.44"></a> -<span class="sourceLineNo">045</span> * Base class for implementing least squares optimizers.<a name="line.45"></a> -<span class="sourceLineNo">046</span> * It handles the boilerplate methods associated to thresholds settings,<a name="line.46"></a> -<span class="sourceLineNo">047</span> * Jacobian and error estimation.<a name="line.47"></a> -<span class="sourceLineNo">048</span> * <br/><a name="line.48"></a> -<span class="sourceLineNo">049</span> * This class constructs the Jacobian matrix of the function argument in method<a name="line.49"></a> -<span class="sourceLineNo">050</span> * {@link BaseAbstractMultivariateVectorOptimizer#optimize(int,<a name="line.50"></a> -<span class="sourceLineNo">051</span> * org.apache.commons.math3.analysis.MultivariateVectorFunction,OptimizationData[])<a name="line.51"></a> -<span class="sourceLineNo">052</span> * optimize} and assumes that the rows of that matrix iterate on the model<a name="line.52"></a> -<span class="sourceLineNo">053</span> * functions while the columns iterate on the parameters; thus, the numbers<a name="line.53"></a> -<span class="sourceLineNo">054</span> * of rows is equal to the dimension of the<a name="line.54"></a> -<span class="sourceLineNo">055</span> * {@link org.apache.commons.math3.optimization.Target Target} while<a name="line.55"></a> -<span class="sourceLineNo">056</span> * the number of columns is equal to the dimension of the<a name="line.56"></a> -<span class="sourceLineNo">057</span> * {@link org.apache.commons.math3.optimization.InitialGuess InitialGuess}.<a name="line.57"></a> -<span class="sourceLineNo">058</span> *<a name="line.58"></a> -<span class="sourceLineNo">059</span> * @deprecated As of 3.1 (to be removed in 4.0).<a name="line.59"></a> -<span class="sourceLineNo">060</span> * @since 1.2<a name="line.60"></a> -<span class="sourceLineNo">061</span> */<a name="line.61"></a> -<span class="sourceLineNo">062</span>@Deprecated<a name="line.62"></a> -<span class="sourceLineNo">063</span>public abstract class AbstractLeastSquaresOptimizer<a name="line.63"></a> -<span class="sourceLineNo">064</span> extends BaseAbstractMultivariateVectorOptimizer<DifferentiableMultivariateVectorFunction><a name="line.64"></a> -<span class="sourceLineNo">065</span> implements DifferentiableMultivariateVectorOptimizer {<a name="line.65"></a> -<span class="sourceLineNo">066</span> /**<a name="line.66"></a> -<span class="sourceLineNo">067</span> * Singularity threshold (cf. {@link #getCovariances(double)}).<a name="line.67"></a> -<span class="sourceLineNo">068</span> * @deprecated As of 3.1.<a name="line.68"></a> -<span class="sourceLineNo">069</span> */<a name="line.69"></a> -<span class="sourceLineNo">070</span> @Deprecated<a name="line.70"></a> -<span class="sourceLineNo">071</span> private static final double DEFAULT_SINGULARITY_THRESHOLD = 1e-14;<a name="line.71"></a> -<span class="sourceLineNo">072</span> /**<a name="line.72"></a> -<span class="sourceLineNo">073</span> * Jacobian matrix of the weighted residuals.<a name="line.73"></a> -<span class="sourceLineNo">074</span> * This matrix is in canonical form just after the calls to<a name="line.74"></a> -<span class="sourceLineNo">075</span> * {@link #updateJacobian()}, but may be modified by the solver<a name="line.75"></a> -<span class="sourceLineNo">076</span> * in the derived class (the {@link LevenbergMarquardtOptimizer<a name="line.76"></a> -<span class="sourceLineNo">077</span> * Levenberg-Marquardt optimizer} does this).<a name="line.77"></a> -<span class="sourceLineNo">078</span> * @deprecated As of 3.1. To be removed in 4.0. Please use<a name="line.78"></a> -<span class="sourceLineNo">079</span> * {@link #computeWeightedJacobian(double[])} instead.<a name="line.79"></a> -<span class="sourceLineNo">080</span> */<a name="line.80"></a> -<span class="sourceLineNo">081</span> @Deprecated<a name="line.81"></a> -<span class="sourceLineNo">082</span> protected double[][] weightedResidualJacobian;<a name="line.82"></a> -<span class="sourceLineNo">083</span> /** Number of columns of the jacobian matrix.<a name="line.83"></a> -<span class="sourceLineNo">084</span> * @deprecated As of 3.1.<a name="line.84"></a> -<span class="sourceLineNo">085</span> */<a name="line.85"></a> -<span class="sourceLineNo">086</span> @Deprecated<a name="line.86"></a> -<span class="sourceLineNo">087</span> protected int cols;<a name="line.87"></a> -<span class="sourceLineNo">088</span> /** Number of rows of the jacobian matrix.<a name="line.88"></a> -<span class="sourceLineNo">089</span> * @deprecated As of 3.1.<a name="line.89"></a> -<span class="sourceLineNo">090</span> */<a name="line.90"></a> -<span class="sourceLineNo">091</span> @Deprecated<a name="line.91"></a> -<span class="sourceLineNo">092</span> protected int rows;<a name="line.92"></a> -<span class="sourceLineNo">093</span> /** Current point.<a name="line.93"></a> -<span class="sourceLineNo">094</span> * @deprecated As of 3.1.<a name="line.94"></a> -<span class="sourceLineNo">095</span> */<a name="line.95"></a> -<span class="sourceLineNo">096</span> @Deprecated<a name="line.96"></a> -<span class="sourceLineNo">097</span> protected double[] point;<a name="line.97"></a> -<span class="sourceLineNo">098</span> /** Current objective function value.<a name="line.98"></a> -<span class="sourceLineNo">099</span> * @deprecated As of 3.1.<a name="line.99"></a> -<span class="sourceLineNo">100</span> */<a name="line.100"></a> -<span class="sourceLineNo">101</span> @Deprecated<a name="line.101"></a> -<span class="sourceLineNo">102</span> protected double[] objective;<a name="line.102"></a> -<span class="sourceLineNo">103</span> /** Weighted residuals<a name="line.103"></a> -<span class="sourceLineNo">104</span> * @deprecated As of 3.1.<a name="line.104"></a> -<span class="sourceLineNo">105</span> */<a name="line.105"></a> -<span class="sourceLineNo">106</span> @Deprecated<a name="line.106"></a> -<span class="sourceLineNo">107</span> protected double[] weightedResiduals;<a name="line.107"></a> -<span class="sourceLineNo">108</span> /** Cost value (square root of the sum of the residuals).<a name="line.108"></a> -<span class="sourceLineNo">109</span> * @deprecated As of 3.1. Field to become "private" in 4.0.<a name="line.109"></a> -<span class="sourceLineNo">110</span> * Please use {@link #setCost(double)}.<a name="line.110"></a> -<span class="sourceLineNo">111</span> */<a name="line.111"></a> -<span class="sourceLineNo">112</span> @Deprecated<a name="line.112"></a> -<span class="sourceLineNo">113</span> protected double cost;<a name="line.113"></a> -<span class="sourceLineNo">114</span> /** Objective function derivatives. */<a name="line.114"></a> -<span class="sourceLineNo">115</span> private MultivariateDifferentiableVectorFunction jF;<a name="line.115"></a> -<span class="sourceLineNo">116</span> /** Number of evaluations of the Jacobian. */<a name="line.116"></a> -<span class="sourceLineNo">117</span> private int jacobianEvaluations;<a name="line.117"></a> -<span class="sourceLineNo">118</span> /** Square-root of the weight matrix. */<a name="line.118"></a> -<span class="sourceLineNo">119</span> private RealMatrix weightMatrixSqrt;<a name="line.119"></a> -<span class="sourceLineNo">120</span><a name="line.120"></a> -<span class="sourceLineNo">121</span> /**<a name="line.121"></a> -<span class="sourceLineNo">122</span> * Simple constructor with default settings.<a name="line.122"></a> -<span class="sourceLineNo">123</span> * The convergence check is set to a {@link<a name="line.123"></a> -<span class="sourceLineNo">124</span> * org.apache.commons.math3.optimization.SimpleVectorValueChecker}.<a name="line.124"></a> -<span class="sourceLineNo">125</span> * @deprecated See {@link org.apache.commons.math3.optimization.SimpleValueChecker#SimpleValueChecker()}<a name="line.125"></a> -<span class="sourceLineNo">126</span> */<a name="line.126"></a> -<span class="sourceLineNo">127</span> @Deprecated<a name="line.127"></a> -<span class="sourceLineNo">128</span> protected AbstractLeastSquaresOptimizer() {}<a name="line.128"></a> -<span class="sourceLineNo">129</span><a name="line.129"></a> -<span class="sourceLineNo">130</span> /**<a name="line.130"></a> -<span class="sourceLineNo">131</span> * @param checker Convergence checker.<a name="line.131"></a> -<span class="sourceLineNo">132</span> */<a name="line.132"></a> -<span class="sourceLineNo">133</span> protected AbstractLeastSquaresOptimizer(ConvergenceChecker<PointVectorValuePair> checker) {<a name="line.133"></a> -<span class="sourceLineNo">134</span> super(checker);<a name="line.134"></a> -<span class="sourceLineNo">135</span> }<a name="line.135"></a> -<span class="sourceLineNo">136</span><a name="line.136"></a> -<span class="sourceLineNo">137</span> /**<a name="line.137"></a> -<span class="sourceLineNo">138</span> * @return the number of evaluations of the Jacobian function.<a name="line.138"></a> -<span class="sourceLineNo">139</span> */<a name="line.139"></a> -<span class="sourceLineNo">140</span> public int getJacobianEvaluations() {<a name="line.140"></a> -<span class="sourceLineNo">141</span> return jacobianEvaluations;<a name="line.141"></a> -<span class="sourceLineNo">142</span> }<a name="line.142"></a> -<span class="sourceLineNo">143</span><a name="line.143"></a> -<span class="sourceLineNo">144</span> /**<a name="line.144"></a> -<span class="sourceLineNo">145</span> * Update the jacobian matrix.<a name="line.145"></a> -<span class="sourceLineNo">146</span> *<a name="line.146"></a> -<span class="sourceLineNo">147</span> * @throws DimensionMismatchException if the Jacobian dimension does not<a name="line.147"></a> -<span class="sourceLineNo">148</span> * match problem dimension.<a name="line.148"></a> -<span class="sourceLineNo">149</span> * @deprecated As of 3.1. Please use {@link #computeWeightedJacobian(double[])}<a name="line.149"></a> -<span class="sourceLineNo">150</span> * instead.<a name="line.150"></a> -<span class="sourceLineNo">151</span> */<a name="line.151"></a> -<span class="sourceLineNo">152</span> @Deprecated<a name="line.152"></a> -<span class="sourceLineNo">153</span> protected void updateJacobian() {<a name="line.153"></a> -<span class="sourceLineNo">154</span> final RealMatrix weightedJacobian = computeWeightedJacobian(point);<a name="line.154"></a> -<span class="sourceLineNo">155</span> weightedResidualJacobian = weightedJacobian.scalarMultiply(-1).getData();<a name="line.155"></a> -<span class="sourceLineNo">156</span> }<a name="line.156"></a> -<span class="sourceLineNo">157</span><a name="line.157"></a> -<span class="sourceLineNo">158</span> /**<a name="line.158"></a> -<span class="sourceLineNo">159</span> * Computes the Jacobian matrix.<a name="line.159"></a> -<span class="sourceLineNo">160</span> *<a name="line.160"></a> -<span class="sourceLineNo">161</span> * @param params Model parameters at which to compute the Jacobian.<a name="line.161"></a> -<span class="sourceLineNo">162</span> * @return the weighted Jacobian: W<sup>1/2</sup> J.<a name="line.162"></a> -<span class="sourceLineNo">163</span> * @throws DimensionMismatchException if the Jacobian dimension does not<a name="line.163"></a> -<span class="sourceLineNo">164</span> * match problem dimension.<a name="line.164"></a> -<span class="sourceLineNo">165</span> * @since 3.1<a name="line.165"></a> -<span class="sourceLineNo">166</span> */<a name="line.166"></a> -<span class="sourceLineNo">167</span> protected RealMatrix computeWeightedJacobian(double[] params) {<a name="line.167"></a> -<span class="sourceLineNo">168</span> ++jacobianEvaluations;<a name="line.168"></a> -<span class="sourceLineNo">169</span><a name="line.169"></a> -<span class="sourceLineNo">170</span> final DerivativeStructure[] dsPoint = new DerivativeStructure[params.length];<a name="line.170"></a> -<span class="sourceLineNo">171</span> final int nC = params.length;<a name="line.171"></a> -<span class="sourceLineNo">172</span> for (int i = 0; i < nC; ++i) {<a name="line.172"></a> -<span class="sourceLineNo">173</span> dsPoint[i] = new DerivativeStructure(nC, 1, i, params[i]);<a name="line.173"></a> -<span class="sourceLineNo">174</span> }<a name="line.174"></a> -<span class="sourceLineNo">175</span> final DerivativeStructure[] dsValue = jF.value(dsPoint);<a name="line.175"></a> -<span class="sourceLineNo">176</span> final int nR = getTarget().length;<a name="line.176"></a> -<span class="sourceLineNo">177</span> if (dsValue.length != nR) {<a name="line.177"></a> -<span class="sourceLineNo">178</span> throw new DimensionMismatchException(dsValue.length, nR);<a name="line.178"></a> -<span class="sourceLineNo">179</span> }<a name="line.179"></a> -<span class="sourceLineNo">180</span> final double[][] jacobianData = new double[nR][nC];<a name="line.180"></a> -<span class="sourceLineNo">181</span> for (int i = 0; i < nR; ++i) {<a name="line.181"></a> -<span class="sourceLineNo">182</span> int[] orders = new int[nC];<a name="line.182"></a> -<span class="sourceLineNo">183</span> for (int j = 0; j < nC; ++j) {<a name="line.183"></a> -<span class="sourceLineNo">184</span> orders[j] = 1;<a name="line.184"></a> -<span class="sourceLineNo">185</span> jacobianData[i][j] = dsValue[i].getPartialDerivative(orders);<a name="line.185"></a> -<span class="sourceLineNo">186</span> orders[j] = 0;<a name="line.186"></a> -<span class="sourceLineNo">187</span> }<a name="line.187"></a> -<span class="sourceLineNo">188</span> }<a name="line.188"></a> -<span class="sourceLineNo">189</span><a name="line.189"></a> -<span class="sourceLineNo">190</span> return weightMatrixSqrt.multiply(MatrixUtils.createRealMatrix(jacobianData));<a name="line.190"></a> -<span class="sourceLineNo">191</span> }<a name="line.191"></a> -<span class="sourceLineNo">192</span><a name="line.192"></a> -<span class="sourceLineNo">193</span> /**<a name="line.193"></a> -<span class="sourceLineNo">194</span> * Update the residuals array and cost function value.<a name="line.194"></a> -<span class="sourceLineNo">195</span> * @throws DimensionMismatchException if the dimension does not match the<a name="line.195"></a> -<span class="sourceLineNo">196</span> * problem dimension.<a name="line.196"></a> -<span class="sourceLineNo">197</span> * @throws org.apache.commons.math3.exception.TooManyEvaluationsException<a name="line.197"></a> -<span class="sourceLineNo">198</span> * if the maximal number of evaluations is exceeded.<a name="line.198"></a> -<span class="sourceLineNo">199</span> * @deprecated As of 3.1. Please use {@link #computeResiduals(double[])},<a name="line.199"></a> -<span class="sourceLineNo">200</span> * {@link #computeObjectiveValue(double[])}, {@link #computeCost(double[])}<a name="line.200"></a> -<span class="sourceLineNo">201</span> * and {@link #setCost(double)} instead.<a name="line.201"></a> -<span class="sourceLineNo">202</span> */<a name="line.202"></a> -<span class="sourceLineNo">203</span> @Deprecated<a name="line.203"></a> -<span class="sourceLineNo">204</span> protected void updateResidualsAndCost() {<a name="line.204"></a> -<span class="sourceLineNo">205</span> objective = computeObjectiveValue(point);<a name="line.205"></a> -<span class="sourceLineNo">206</span> final double[] res = computeResiduals(objective);<a name="line.206"></a> -<span class="sourceLineNo">207</span><a name="line.207"></a> -<span class="sourceLineNo">208</span> // Compute cost.<a name="line.208"></a> -<span class="sourceLineNo">209</span> cost = computeCost(res);<a name="line.209"></a> -<span class="sourceLineNo">210</span><a name="line.210"></a> -<span class="sourceLineNo">211</span> // Compute weighted residuals.<a name="line.211"></a> -<span class="sourceLineNo">212</span> final ArrayRealVector residuals = new ArrayRealVector(res);<a name="line.212"></a> -<span class="sourceLineNo">213</span> weightedResiduals = weightMatrixSqrt.operate(residuals).toArray();<a name="line.213"></a> -<span class="sourceLineNo">214</span> }<a name="line.214"></a> -<span class="sourceLineNo">215</span><a name="line.215"></a> -<span class="sourceLineNo">216</span> /**<a name="line.216"></a> -<span class="sourceLineNo">217</span> * Computes the cost.<a name="line.217"></a> -<span class="sourceLineNo">218</span> *<a name="line.218"></a> -<span class="sourceLineNo">219</span> * @param residuals Residuals.<a name="line.219"></a> -<span class="sourceLineNo">220</span> * @return the cost.<a name="line.220"></a> -<span class="sourceLineNo">221</span> * @see #computeResiduals(double[])<a name="line.221"></a> -<span class="sourceLineNo">222</span> * @since 3.1<a name="line.222"></a> -<span class="sourceLineNo">223</span> */<a name="line.223"></a> -<span class="sourceLineNo">224</span> protected double computeCost(double[] residuals) {<a name="line.224"></a> -<span class="sourceLineNo">225</span> final ArrayRealVector r = new ArrayRealVector(residuals);<a name="line.225"></a> -<span class="sourceLineNo">226</span> return FastMath.sqrt(r.dotProduct(getWeight().operate(r)));<a name="line.226"></a> -<span class="sourceLineNo">227</span> }<a name="line.227"></a> -<span class="sourceLineNo">228</span><a name="line.228"></a> -<span class="sourceLineNo">229</span> /**<a name="line.229"></a> -<span class="sourceLineNo">230</span> * Get the Root Mean Square value.<a name="line.230"></a> -<span class="sourceLineNo">231</span> * Get the Root Mean Square value, i.e. the root of the arithmetic<a name="line.231"></a> -<span class="sourceLineNo">232</span> * mean of the square of all weighted residuals. This is related to the<a name="line.232"></a> -<span class="sourceLineNo">233</span> * criterion that is minimized by the optimizer as follows: if<a name="line.233"></a> -<span class="sourceLineNo">234</span> * <em>c</em> if the criterion, and <em>n</em> is the number of<a name="line.234"></a> -<span class="sourceLineNo">235</span> * measurements, then the RMS is <em>sqrt (c/n)</em>.<a name="line.235"></a> -<span class="sourceLineNo">236</span> *<a name="line.236"></a> -<span class="sourceLineNo">237</span> * @return RMS value<a name="line.237"></a> -<span class="sourceLineNo">238</span> */<a name="line.238"></a> -<span class="sourceLineNo">239</span> public double getRMS() {<a name="line.239"></a> -<span class="sourceLineNo">240</span> return FastMath.sqrt(getChiSquare() / rows);<a name="line.240"></a> -<span class="sourceLineNo">241</span> }<a name="line.241"></a> -<span class="sourceLineNo">242</span><a name="line.242"></a> -<span class="sourceLineNo">243</span> /**<a name="line.243"></a> -<span class="sourceLineNo">244</span> * Get a Chi-Square-like value assuming the N residuals follow N<a name="line.244"></a> -<span class="sourceLineNo">245</span> * distinct normal distributions centered on 0 and whose variances are<a name="line.245"></a> -<span class="sourceLineNo">246</span> * the reciprocal of the weights.<a name="line.246"></a> -<span class="sourceLineNo">247</span> * @return chi-square value<a name="line.247"></a> -<span class="sourceLineNo">248</span> */<a name="line.248"></a> -<span class="sourceLineNo">249</span> public double getChiSquare() {<a name="line.249"></a> -<span class="sourceLineNo">250</span> return cost * cost;<a name="line.250"></a> -<span class="sourceLineNo">251</span> }<a name="line.251"></a> -<span class="sourceLineNo">252</span><a name="line.252"></a> -<span class="sourceLineNo">253</span> /**<a name="line.253"></a> -<span class="sourceLineNo">254</span> * Gets the square-root of the weight matrix.<a name="line.254"></a> -<span class="sourceLineNo">255</span> *<a name="line.255"></a> -<span class="sourceLineNo">256</span> * @return the square-root of the weight matrix.<a name="line.256"></a> -<span class="sourceLineNo">257</span> * @since 3.1<a name="line.257"></a> -<span class="sourceLineNo">258</span> */<a name="line.258"></a> -<span class="sourceLineNo">259</span> public RealMatrix getWeightSquareRoot() {<a name="line.259"></a> -<span class="sourceLineNo">260</span> return weightMatrixSqrt.copy();<a name="line.260"></a> -<span class="sourceLineNo">261</span> }<a name="line.261"></a> -<span class="sourceLineNo">262</span><a name="line.262"></a> -<span class="sourceLineNo">263</span> /**<a name="line.263"></a> -<span class="sourceLineNo">264</span> * Sets the cost.<a name="line.264"></a> -<span class="sourceLineNo">265</span> *<a name="line.265"></a> -<span class="sourceLineNo">266</span> * @param cost Cost value.<a name="line.266"></a> -<span class="sourceLineNo">267</span> * @since 3.1<a name="line.267"></a> -<span class="sourceLineNo">268</span> */<a name="line.268"></a> -<span class="sourceLineNo">269</span> protected void setCost(double cost) {<a name="line.269"></a> -<span class="sourceLineNo">270</span> this.cost = cost;<a name="line.270"></a> -<span class="sourceLineNo">271</span> }<a name="line.271"></a> -<span class="sourceLineNo">272</span><a name="line.272"></a> -<span class="sourceLineNo">273</span> /**<a name="line.273"></a> -<span class="sourceLineNo">274</span> * Get the covariance matrix of the optimized parameters.<a name="line.274"></a> -<span class="sourceLineNo">275</span> *<a name="line.275"></a> -<span class="sourceLineNo">276</span> * @return the covariance matrix.<a name="line.276"></a> -<span class="sourceLineNo">277</span> * @throws org.apache.commons.math3.linear.SingularMatrixException<a name="line.277"></a> -<span class="sourceLineNo">278</span> * if the covariance matrix cannot be computed (singular problem).<a name="line.278"></a> -<span class="sourceLineNo">279</span> * @see #getCovariances(double)<a name="line.279"></a> -<span class="sourceLineNo">280</span> * @deprecated As of 3.1. Please use {@link #computeCovariances(double[],double)}<a name="line.280"></a> -<span class="sourceLineNo">281</span> * instead.<a name="line.281"></a> -<span class="sourceLineNo">282</span> */<a name="line.282"></a> -<span class="sourceLineNo">283</span> @Deprecated<a name="line.283"></a> -<span class="sourceLineNo">284</span> public double[][] getCovariances() {<a name="line.284"></a> -<span class="sourceLineNo">285</span> return getCovariances(DEFAULT_SINGULARITY_THRESHOLD);<a name="line.285"></a> -<span class="sourceLineNo">286</span> }<a name="line.286"></a> -<span class="sourceLineNo">287</span><a name="line.287"></a> -<span class="sourceLineNo">288</span> /**<a name="line.288"></a> -<span class="sourceLineNo">289</span> * Get the covariance matrix of the optimized parameters.<a name="line.289"></a> -<span class="sourceLineNo">290</span> * <br/><a name="line.290"></a> -<span class="sourceLineNo">291</span> * Note that this operation involves the inversion of the<a name="line.291"></a> -<span class="sourceLineNo">292</span> * <code>J<sup>T</sup>J</code> matrix, where {@code J} is the<a name="line.292"></a> -<span class="sourceLineNo">293</span> * Jacobian matrix.<a name="line.293"></a> -<span class="sourceLineNo">294</span> * The {@code threshold} parameter is a way for the caller to specify<a name="line.294"></a> -<span class="sourceLineNo">295</span> * that the result of this computation should be considered meaningless,<a name="line.295"></a> -<span class="sourceLineNo">296</span> * and thus trigger an exception.<a name="line.296"></a> -<span class="sourceLineNo">297</span> *<a name="line.297"></a> -<span class="sourceLineNo">298</span> * @param threshold Singularity threshold.<a name="line.298"></a> -<span class="sourceLineNo">299</span> * @return the covariance matrix.<a name="line.299"></a> -<span class="sourceLineNo">300</span> * @throws org.apache.commons.math3.linear.SingularMatrixException<a name="line.300"></a> -<span class="sourceLineNo">301</span> * if the covariance matrix cannot be computed (singular problem).<a name="line.301"></a> -<span class="sourceLineNo">302</span> * @deprecated As of 3.1. Please use {@link #computeCovariances(double[],double)}<a name="line.302"></a> -<span class="sourceLineNo">303</span> * instead.<a name="line.303"></a> -<span class="sourceLineNo">304</span> */<a name="line.304"></a> -<span class="sourceLineNo">305</span> @Deprecated<a name="line.305"></a> -<span class="sourceLineNo">306</span> public double[][] getCovariances(double threshold) {<a name="line.306"></a> -<span class="sourceLineNo">307</span> return computeCovariances(point, threshold);<a name="line.307"></a> -<span class="sourceLineNo">308</span> }<a name="line.308"></a> -<span class="sourceLineNo">309</span><a name="line.309"></a> -<span class="sourceLineNo">310</span> /**<a name="line.310"></a> -<span class="sourceLineNo">311</span> * Get the covariance matrix of the optimized parameters.<a name="line.311"></a> -<span class="sourceLineNo">312</span> * <br/><a name="line.312"></a> -<span class="sourceLineNo">313</span> * Note that this operation involves the inversion of the<a name="line.313"></a> -<span class="sourceLineNo">314</span> * <code>J<sup>T</sup>J</code> matrix, where {@code J} is the<a name="line.314"></a> -<span class="sourceLineNo">315</span> * Jacobian matrix.<a name="line.315"></a> -<span class="sourceLineNo">316</span> * The {@code threshold} parameter is a way for the caller to specify<a name="line.316"></a> -<span class="sourceLineNo">317</span> * that the result of this computation should be considered meaningless,<a name="line.317"></a> -<span class="sourceLineNo">318</span> * and thus trigger an exception.<a name="line.318"></a> -<span class="sourceLineNo">319</span> *<a name="line.319"></a> -<span class="sourceLineNo">320</span> * @param params Model parameters.<a name="line.320"></a> -<span class="sourceLineNo">321</span> * @param threshold Singularity threshold.<a name="line.321"></a> -<span class="sourceLineNo">322</span> * @return the covariance matrix.<a name="line.322"></a> -<span class="sourceLineNo">323</span> * @throws org.apache.commons.math3.linear.SingularMatrixException<a name="line.323"></a> -<span class="sourceLineNo">324</span> * if the covariance matrix cannot be computed (singular problem).<a name="line.324"></a> -<span class="sourceLineNo">325</span> * @since 3.1<a name="line.325"></a> -<span class="sourceLineNo">326</span> */<a name="line.326"></a> -<span class="sourceLineNo">327</span> public double[][] computeCovariances(double[] params,<a name="line.327"></a> -<span class="sourceLineNo">328</span> double threshold) {<a name="line.328"></a> -<span class="sourceLineNo">329</span> // Set up the Jacobian.<a name="line.329"></a> -<span class="sourceLineNo">330</span> final RealMatrix j = computeWeightedJacobian(params);<a name="line.330"></a> -<span class="sourceLineNo">331</span><a name="line.331"></a> -<span class="sourceLineNo">332</span> // Compute transpose(J)J.<a name="line.332"></a> -<span class="sourceLineNo">333</span> final RealMatrix jTj = j.transpose().multiply(j);<a name="line.333"></a> -<span class="sourceLineNo">334</span><a name="line.334"></a> -<span class="sourceLineNo">335</span> // Compute the covariances matrix.<a name="line.335"></a> -<span class="sourceLineNo">336</span> final DecompositionSolver solver<a name="line.336"></a> -<span class="sourceLineNo">337</span> = new QRDecomposition(jTj, threshold).getSolver();<a name="line.337"></a> -<span class="sourceLineNo">338</span> return solver.getInverse().getData();<a name="line.338"></a> -<span class="sourceLineNo">339</span> }<a name="line.339"></a> -<span class="sourceLineNo">340</span><a name="line.340"></a> -<span class="sourceLineNo">341</span> /**<a name="line.341"></a> -<span class="sourceLineNo">342</span> * <p><a name="line.342"></a> -<span class="sourceLineNo">343</span> * Returns an estimate of the standard deviation of each parameter. The<a name="line.343"></a> -<span class="sourceLineNo">344</span> * returned values are the so-called (asymptotic) standard errors on the<a name="line.344"></a> -<span class="sourceLineNo">345</span> * parameters, defined as {@code sd(a[i]) = sqrt(S / (n - m) * C[i][i])},<a name="line.345"></a> -<span class="sourceLineNo">346</span> * where {@code a[i]} is the optimized value of the {@code i}-th parameter,<a name="line.346"></a> -<span class="sourceLineNo">347</span> * {@code S} is the minimized value of the sum of squares objective function<a name="line.347"></a> -<span class="sourceLineNo">348</span> * (as returned by {@link #getChiSquare()}), {@code n} is the number of<a name="line.348"></a> -<span class="sourceLineNo">349</span> * observations, {@code m} is the number of parameters and {@code C} is the<a name="line.349"></a> -<span class="sourceLineNo">350</span> * covariance matrix.<a name="line.350"></a> -<span class="sourceLineNo">351</span> * </p><a name="line.351"></a> -<span class="sourceLineNo">352</span> * <p><a name="line.352"></a> -<span class="sourceLineNo">353</span> * See also<a name="line.353"></a> -<span class="sourceLineNo">354</span> * <a href="http://en.wikipedia.org/wiki/Least_squares">Wikipedia</a>,<a name="line.354"></a> -<span class="sourceLineNo">355</span> * or<a name="line.355"></a> -<span class="sourceLineNo">356</span> * <a href="http://mathworld.wolfram.com/LeastSquaresFitting.html">MathWorld</a>,<a name="line.356"></a> -<span class="sourceLineNo">357</span> * equations (34) and (35) for a particular case.<a name="line.357"></a> -<span class="sourceLineNo">358</span> * </p><a name="line.358"></a> -<span class="sourceLineNo">359</span> *<a name="line.359"></a> -<span class="sourceLineNo">360</span> * @return an estimate of the standard deviation of the optimized parameters<a name="line.360"></a> -<span class="sourceLineNo">361</span> * @throws org.apache.commons.math3.linear.SingularMatrixException<a name="line.361"></a> -<span class="sourceLineNo">362</span> * if the covariance matrix cannot be computed.<a name="line.362"></a> -<span class="sourceLineNo">363</span> * @throws NumberIsTooSmallException if the number of degrees of freedom is not<a name="line.363"></a> -<span class="sourceLineNo">364</span> * positive, i.e. the number of measurements is less or equal to the number of<a name="line.364"></a> -<span class="sourceLineNo">365</span> * parameters.<a name="line.365"></a> -<span class="sourceLineNo">366</span> * @deprecated as of version 3.1, {@link #computeSigma(double[],double)} should be used<a name="line.366"></a> -<span class="sourceLineNo">367</span> * instead. It should be emphasized that {@code guessParametersErrors} and<a name="line.367"></a> -<span class="sourceLineNo">368</span> * {@code computeSigma} are <em>not</em> strictly equivalent.<a name="line.368"></a> -<span class="sourceLineNo">369</span> */<a name="line.369"></a> -<span class="sourceLineNo">370</span> @Deprecated<a name="line.370"></a> -<span class="sourceLineNo">371</span> public double[] guessParametersErrors() {<a name="line.371"></a> -<span class="sourceLineNo">372</span> if (rows <= cols) {<a name="line.372"></a> -<span class="sourceLineNo">373</span> throw new NumberIsTooSmallException(LocalizedFormats.NO_DEGREES_OF_FREEDOM,<a name="line.373"></a> -<span class="sourceLineNo">374</span> rows, cols, false);<a name="line.374"></a> -<span class="sourceLineNo">375</span> }<a name="line.375"></a> -<span class="sourceLineNo">376</span> double[] errors = new double[cols];<a name="line.376"></a> -<span class="sourceLineNo">377</span> final double c = FastMath.sqrt(getChiSquare() / (rows - cols));<a name="line.377"></a> -<span class="sourceLineNo">378</span> double[][] covar = computeCovariances(point, 1e-14);<a name="line.378"></a> -<span class="sourceLineNo">379</span> for (int i = 0; i < errors.length; ++i) {<a name="line.379"></a> -<span class="sourceLineNo">380</span> errors[i] = FastMath.sqrt(covar[i][i]) * c;<a name="line.380"></a> -<span class="sourceLineNo">381</span> }<a name="line.381"></a> -<span class="sourceLineNo">382</span> return errors;<a name="line.382"></a> -<span class="sourceLineNo">383</span> }<a name="line.383"></a> -<span class="sourceLineNo">384</span><a name="line.384"></a> -<span class="sourceLineNo">385</span> /**<a name="line.385"></a> -<span class="sourceLineNo">386</span> * Computes an estimate of the standard deviation of the parameters. The<a name="line.386"></a> -<span class="sourceLineNo">387</span> * returned values are the square root of the diagonal coefficients of the<a name="line.387"></a> -<span class="sourceLineNo">388</span> * covariance matrix, {@code sd(a[i]) ~= sqrt(C[i][i])}, where {@code a[i]}<a name="line.388"></a> -<span class="sourceLineNo">389</span> * is the optimized value of the {@code i}-th parameter, and {@code C} is<a name="line.389"></a> -<span class="sourceLineNo">390</span> * the covariance matrix.<a name="line.390"></a> -<span class="sourceLineNo">391</span> *<a name="line.391"></a> -<span class="sourceLineNo">392</span> * @param params Model parameters.<a name="line.392"></a> -<span class="sourceLineNo">393</span> * @param covarianceSingularityThreshold Singularity threshold (see<a name="line.393"></a> -<span class="sourceLineNo">394</span> * {@link #computeCovariances(double[],double) computeCovariances}).<a name="line.394"></a> -<span class="sourceLineNo">395</span> * @return an estimate of the standard deviation of the optimized parameters<a name="line.395"></a> -<span class="sourceLineNo">396</span> * @throws org.apache.commons.math3.linear.SingularMatrixException<a name="line.396"></a> -<span class="sourceLineNo">397</span> * if the covariance matrix cannot be computed.<a name="line.397"></a> -<span class="sourceLineNo">398</span> * @since 3.1<a name="line.398"></a> -<span class="sourceLineNo">399</span> */<a name="line.399"></a> -<span class="sourceLineNo">400</span> public double[] computeSigma(double[] params,<a name="line.400"></a> -<span class="sourceLineNo">401</span> double covarianceSingularityThreshold) {<a name="line.401"></a> -<span class="sourceLineNo">402</span> final int nC = params.length;<a name="line.402"></a> -<span class="sourceLineNo">403</span> final double[] sig = new double[nC];<a name="line.403"></a> -<span class="sourceLineNo">404</span> final double[][] cov = computeCovariances(params, covarianceSingularityThreshold);<a name="line.404"></a> -<span class="sourceLineNo">405</span> for (int i = 0; i < nC; ++i) {<a name="line.405"></a> -<span class="sourceLineNo">406</span> sig[i] = FastMath.sqrt(cov[i][i]);<a name="line.406"></a> -<span class="sourceLineNo">407</span> }<a name="line.407"></a> -<span class="sourceLineNo">408</span> return sig;<a name="line.408"></a> -<span class="sourceLineNo">409</span> }<a name="line.409"></a> -<span class="sourceLineNo">410</span><a name="line.410"></a> -<span class="sourceLineNo">411</span> /** {@inheritDoc}<a name="line.411"></a> -<span class="sourceLineNo">412</span> * @deprecated As of 3.1. Please use<a name="line.412"></a> -<span class="sourceLineNo">413</span> * {@link BaseAbstractMultivariateVectorOptimizer#optimize(int,<a name="line.413"></a> -<span class="sourceLineNo">414</span> * org.apache.commons.math3.analysis.MultivariateVectorFunction,OptimizationData[])<a name="line.414"></a> -<span class="sourceLineNo">415</span> * optimize(int,MultivariateDifferentiableVectorFunction,OptimizationData...)}<a name="line.415"></a> -<span class="sourceLineNo">416</span> * instead.<a name="line.416"></a> -<span class="sourceLineNo">417</span> */<a name="line.417"></a> -<span class="sourceLineNo">418</span> @Override<a name="line.418"></a> -<span class="sourceLineNo">419</span> @Deprecated<a name="line.419"></a> -<span class="sourceLineNo">420</span> public PointVectorValuePair optimize(int maxEval,<a name="line.420"></a> -<span class="sourceLineNo">421</span> final DifferentiableMultivariateVectorFunction f,<a name="line.421"></a> -<span class="sourceLineNo">422</span> final double[] target, final double[] weights,<a name="line.422"></a> -<span class="sourceLineNo">423</span> final double[] startPoint) {<a name="line.423"></a> -<span class="sourceLineNo">424</span> return optimizeInternal(maxEval,<a name="line.424"></a> -<span class="sourceLineNo">425</span> FunctionUtils.toMultivariateDifferentiableVectorFunction(f),<a name="line.425"></a> -<span class="sourceLineNo">426</span> new Target(target),<a name="line.426"></a> -<span class="sourceLineNo">427</span> new Weight(weights),<a name="line.427"></a> -<span class="sourceLineNo">428</span> new InitialGuess(startPoint));<a name="line.428"></a> -<span class="sourceLineNo">429</span> }<a name="line.429"></a> -<span class="sourceLineNo">430</span><a name="line.430"></a> -<span class="sourceLineNo">431</span> /**<a name="line.431"></a> -<span class="sourceLineNo">432</span> * Optimize an objective function.<a name="line.432"></a> -<span class="sourceLineNo">433</span> * Optimization is considered to be a weighted least-squares minimization.<a name="line.433"></a> -<span class="sourceLineNo">434</span> * The cost function to be minimized is<a name="line.434"></a> -<span class="sourceLineNo">435</span> * <code>&sum;weight<sub>i</sub>(objective<sub>i</sub> - target<sub>i</sub>)<sup>2</sup></code><a name="line.435"></a> -<span class="sourceLineNo">436</span> *<a name="line.436"></a> -<span class="sourceLineNo">437</span> * @param f Objective function.<a name="line.437"></a> -<span class="sourceLineNo">438</span> * @param target Target value for the objective functions at optimum.<a name="line.438"></a> -<span class="sourceLineNo">439</span> * @param weights Weights for the least squares cost computation.<a name="line.439"></a> -<span class="sourceLineNo">440</span> * @param startPoint Start point for optimization.<a name="line.440"></a> -<span class="sourceLineNo">441</span> * @return the point/value pair giving the optimal value for objective<a name="line.441"></a> -<span class="sourceLineNo">442</span> * function.<a name="line.442"></a> -<span class="sourceLineNo">443</span> * @param maxEval Maximum number of function evaluations.<a name="line.443"></a> -<span class="sourceLineNo">444</span> * @throws org.apache.commons.math3.exception.DimensionMismatchException<a name="line.444"></a> -<span class="sourceLineNo">445</span> * if the start point dimension is wrong.<a name="line.445"></a> -<span class="sourceLineNo">446</span> * @throws org.apache.commons.math3.exception.TooManyEvaluationsException<a name="line.446"></a> -<span class="sourceLineNo">447</span> * if the maximal number of evaluations is exceeded.<a name="line.447"></a> -<span class="sourceLineNo">448</span> * @throws org.apache.commons.math3.exception.NullArgumentException if<a name="line.448"></a> -<span class="sourceLineNo">449</span> * any argument is {@code null}.<a name="line.449"></a> -<span class="sourceLineNo">450</span> * @deprecated As of 3.1. Please use<a name="line.450"></a> -<span class="sourceLineNo">451</span> * {@link BaseAbstractMultivariateVectorOptimizer#optimize(int,<a name="line.451"></a> -<span class="sourceLineNo">452</span> * org.apache.commons.math3.analysis.MultivariateVectorFunction,OptimizationData[])<a name="line.452"></a> -<span class="sourceLineNo">453</span> * optimize(int,MultivariateDifferentiableVectorFunction,OptimizationData...)}<a name="line.453"></a> -<span class="sourceLineNo">454</span> * instead.<a name="line.454"></a> -<span class="sourceLineNo">455</span> */<a name="line.455"></a> -<span class="sourceLineNo">456</span> @Deprecated<a name="line.456"></a> -<span class="sourceLineNo">457</span> public PointVectorValuePair optimize(final int maxEval,<a name="line.457"></a> -<span class="sourceLineNo">458</span> final MultivariateDifferentiableVectorFunction f,<a name="line.458"></a> -<span class="sourceLineNo">459</span> final double[] target, final double[] weights,<a name="line.459"></a> -<span class="sourceLineNo">460</span> final double[] startPoint) {<a name="line.460"></a> -<span class="sourceLineNo">461</span> return optimizeInternal(maxEval, f,<a name="line.461"></a> -<span class="sourceLineNo">462</span> new Target(target),<a name="line.462"></a> -<span class="sourceLineNo">463</span> new Weight(weights),<a name="line.463"></a> -<span class="sourceLineNo">464</span> new InitialGuess(startPoint));<a name="line.464"></a> -<span class="sourceLineNo">465</span> }<a name="line.465"></a> -<span class="sourceLineNo">466</span><a name="line.466"></a> -<span class="sourceLineNo">467</span> /**<a name="line.467"></a> -<span class="sourceLineNo">468</span> * Optimize an objective function.<a name="line.468"></a> -<span class="sourceLineNo">469</span> * Optimization is considered to be a weighted least-squares minimization.<a name="line.469"></a> -<span class="sourceLineNo">470</span> * The cost function to be minimized is<a name="line.470"></a> -<span class="sourceLineNo">471</span> * <code>&sum;weight<sub>i</sub>(objective<sub>i</sub> - target<sub>i</sub>)<sup>2</sup></code><a name="line.471"></a> -<span class="sourceLineNo">472</span> *<a name="line.472"></a> -<span class="sourceLineNo">473</span> * @param maxEval Allowed number of evaluations of the objective function.<a name="line.473"></a> -<span class="sourceLineNo">474</span> * @param f Objective function.<a name="line.474"></a> -<span class="sourceLineNo">475</span> * @param optData Optimization data. The following data will be looked for:<a name="line.475"></a> -<span class="sourceLineNo">476</span> * <ul><a name="line.476"></a> -<span class="sourceLineNo">477</span> * <li>{@link Target}</li><a name="line.477"></a> -<span class="sourceLineNo">478</span> * <li>{@link Weight}</li><a name="line.478"></a> -<span class="sourceLineNo">479</span> * <li>{@link InitialGuess}</li><a name="line.479"></a> -<span class="sourceLineNo">480</span> * </ul><a name="line.480"></a> -<span class="sourceLineNo">481</span> * @return the point/value pair giving the optimal value of the objective<a name="line.481"></a> -<span class="sourceLineNo">482</span> * function.<a name="line.482"></a> -<span class="sourceLineNo">483</span> * @throws org.apache.commons.math3.exception.TooManyEvaluationsException if<a name="line.483"></a> -<span class="sourceLineNo">484</span> * the maximal number of evaluations is exceeded.<a name="line.484"></a> -<span class="sourceLineNo">485</span> * @throws DimensionMismatchException if the target, and weight arguments<a name="line.485"></a> -<span class="sourceLineNo">486</span> * have inconsistent dimensions.<a name="line.486"></a> -<span class="sourceLineNo">487</span> * @see BaseAbstractMultivariateVectorOptimizer#optimizeInternal(int,<a name="line.487"></a> -<span class="sourceLineNo">488</span> * org.apache.commons.math3.analysis.MultivariateVectorFunction,OptimizationData[])<a name="line.488"></a> -<span class="sourceLineNo">489</span> * @since 3.1<a name="line.489"></a> -<span class="sourceLineNo">490</span> * @deprecated As of 3.1. Override is necessary only until this class's generic<a name="line.490"></a> -<span class="sourceLineNo">491</span> * argument is changed to {@code MultivariateDifferentiableVectorFunction}.<a name="line.491"></a> -<span class="sourceLineNo">492</span> */<a name="line.492"></a> -<span class="sourceLineNo">493</span> @Deprecated<a name="line.493"></a> -<span class="sourceLineNo">494</span> protected PointVectorValuePair optimizeInternal(final int maxEval,<a name="line.494"></a> -<span class="sourceLineNo">495</span> final MultivariateDifferentiableVectorFunction f,<a name="line.495"></a> -<span class="sourceLineNo">496</span> OptimizationData... optData) {<a name="line.496"></a> -<span class="sourceLineNo">497</span> // XXX Conversion will be removed when the generic argument of the<a name="line.497"></a> -<span class="sourceLineNo">498</span> // base class becomes "MultivariateDifferentiableVectorFunction".<a name="line.498"></a> -<span class="sourceLineNo">499</span> return super.optimizeInternal(maxEval, FunctionUtils.toDifferentiableMultivariateVectorFunction(f), optData);<a name="line.499"></a> -<span class="sourceLineNo">500</span> }<a name="line.500"></a> -<span class="sourceLineNo">501</span><a name="line.501"></a> -<span class="sourceLineNo">502</span> /** {@inheritDoc} */<a name="line.502"></a> -<span class="sourceLineNo">503</span> @Override<a name="line.503"></a> -<span class="sourceLineNo">504</span> protected void setUp() {<a name="line.504"></a> -<span class="sourceLineNo">505</span> super.setUp();<a name="line.505"></a> -<span class="sourceLineNo">506</span><a name="line.506"></a> -<span class="sourceLineNo">507</span> // Reset counter.<a name="line.507"></a> -<span class="sourceLineNo">508</span> jacobianEvaluations = 0;<a name="line.508"></a> -<span class="sourceLineNo">509</span><a name="line.509"></a> -<span class="sourceLineNo">510</span> // Square-root of the weight matrix.<a name="line.510"></a> -<span class="sourceLineNo">511</span> weightMatrixSqrt = squareRoot(getWeight());<a name="line.511"></a> -<span class="sourceLineNo">512</span><a name="line.512"></a> -<span class="sourceLineNo">513</span> // Store least squares problem characteristics.<a name="line.513"></a> -<span class="sourceLineNo">514</span> // XXX The conversion won't be necessary when the generic argument of<a name="line.514"></a> -<span class="sourceLineNo">515</span> // the base class becomes "MultivariateDifferentiableVectorFunction".<a name="line.515"></a> -<span class="sourceLineNo">516</span> // XXX "jF" is not strictly necessary anymore but is currently more<a name="line.516"></a> -<span class="sourceLineNo">517</span> // efficient than converting the value returned from "getObjectiveFunction()"<a name="line.517"></a> -<span class="sourceLineNo">518</span> // every time it is used.<a name="line.518"></a> -<span class="sourceLineNo">519</span> jF = FunctionUtils.toMultivariateDifferentiableVectorFunction((DifferentiableMultivariateVectorFunction) getObjectiveFunction());<a name="line.519"></a> -<span class="sourceLineNo">520</span><a name="line.520"></a> -<span class="sourceLineNo">521</span> // Arrays shared with "private" and "protected" methods.<a name="line.521"></a> -<span class="sourceLineNo">522</span> point = getStartPoint();<a name="line.522"></a> -<span class="sourceLineNo">523</span> rows = getTarget().length;<a name="line.523"></a> -<span class="sourceLineNo">524</span> cols = point.length;<a name="line.524"></a> -<span class="sourceLineNo">525</span> }<a name="line.525"></a> -<span class="sourceLineNo">526</span><a name="line.526"></a> -<span class="sourceLineNo">527</span> /**<a name="line.527"></a> -<span class="sourceLineNo">528</span> * Computes the residuals.<a name="line.528"></a> -<span class="sourceLineNo">529</span> * The residual is the difference between the observed (target)<a name="line.529"></a> -<span class="sourceLineNo">530</span> * values and the model (objective function) value.<a name="line.530"></a> -<span class="sourceLineNo">531</span> * There is one residual for each element of the vector-valued<a name="line.531"></a> -<span class="sourceLineNo">532</span> * function.<a name="line.532"></a> -<span class="sourceLineNo">533</span> *<a name="line.533"></a> -<span class="sourceLineNo">534</span> * @param objectiveValue Value of the the objective function. This is<a name="line.534"></a> -<span class="sourceLineNo">535</span> * the value returned from a call to<a name="line.535"></a> -<span class="sourceLineNo">536</span> * {@link #computeObjectiveValue(double[]) computeObjectiveValue}<a name="line.536"></a> -<span class="sourceLineNo">537</span> * (whose array argument contains the model parameters).<a name="line.537"></a> -<span class="sourceLineNo">538</span> * @return the residuals.<a name="line.538"></a> -<span class="sourceLineNo">539</span> * @throws DimensionMismatchException if {@code params} has a wrong<a name="line.539"></a> -<span class="sourceLineNo">540</span> * length.<a name="line.540"></a> -<span class="sourceLineNo">541</span> * @since 3.1<a name="line.541"></a> -<span class="sourceLineNo">542</span> */<a name="line.542"></a> -<span class="sourceLineNo">543</span> protected double[] computeResiduals(double[] objectiveValue) {<a name="line.543"></a> -<span class="sourceLineNo">544</span> final double[] target = getTarget();<a name="line.544"></a> -<span class="sourceLineNo">545</span> if (objectiveValue.length != target.length) {<a name="line.545"></a> -<span class="sourceLineNo">546</span> throw new DimensionMismatchException(target.length,<a name="line.546"></a> -<span class="sourceLineNo">547</span> objectiveValue.length);<a name="line.547"></a> -<span class="sourceLineNo">548</span> }<a name="line.548"></a> -<span class="sourceLineNo">549</span><a name="line.549"></a> -<span class="sourceLineNo">550</span> final double[] residuals = new double[target.length];<a name="line.550"></a> -<span class="sourceLineNo">551</span> for (int i = 0; i < target.length; i++) {<a name="line.551"></a> -<span class="sourceLineNo">552</span> residuals[i] = target[i] - objectiveValue[i];<a name="line.552"></a> -<span class="sourceLineNo">553</span> }<a name="line.553"></a> -<span class="sourceLineNo">554</span><a name="line.554"></a> -<span class="sourceLineNo">555</span> return residuals;<a name="line.555"></a> -<span class="sourceLineNo">556</span> }<a name="line.556"></a> -<span class="sourceLineNo">557</span><a name="line.557"></a> -<span class="sourceLineNo">558</span> /**<a name="line.558"></a> -<span class="sourceLineNo">559</span> * Computes the square-root of the weight matrix.<a name="line.559"></a> -<span class="sourceLineNo">560</span> *<a name="line.560"></a> -<span class="sourceLineNo">561</span> * @param m Symmetric, positive-definite (weight) matrix.<a name="line.561"></a> -<span class="sourceLineNo">562</span> * @return the square-root of the weight matrix.<a name="line.562"></a> -<span class="sourceLineNo">563</span> */<a name="line.563"></a> -<span class="sourceLineNo">564</span> private RealMatrix squareRoot(RealMatrix m) {<a name="line.564"></a> -<span class="sourceLineNo">565</span> if (m instanceof DiagonalMatrix) {<a name="line.565"></a> -<span class="sourceLineNo">566</span> final int dim = m.getRowDimension();<a name="line.566"></a> -<span class="sourceLineNo">567</span> final RealMatrix sqrtM = new DiagonalMatrix(dim);<a name="line.567"></a> -<span class="sourceLineNo">568</span> for (int i = 0; i < dim; i++) {<a name="line.568"></a> -<span class="sourceLineNo">569</span> sqrtM.setEntry(i, i, FastMath.sqrt(m.getEntry(i, i)));<a name="line.569"></a> -<span class="sourceLineNo">570</span> }<a name="line.570"></a> -<span class="sourceLineNo">571</span> return sqrtM;<a name="line.571"></a> -<span class="sourceLineNo">572</span> } else {<a name="line.572"></a> -<span class="sourceLineNo">573</span> final EigenDecomposition dec = new EigenDecomposition(m);<a name="line.573"></a> -<span class="sourceLineNo">574</span> return dec.getSquareRoot();<a name="line.574"></a> -<span class="sourceLineNo">575</span> }<a name="line.575"></a> -<span class="sourceLineNo">576</span> }<a name="line.576"></a> -<span class="sourceLineNo">577</span>}<a name="line.577"></a> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -</pre> -</div> -</body> -</html>
http://git-wip-us.apache.org/repos/asf/commons-complex/blob/b3576eeb/site-content/.svn/pristine/02/025dd274e61ae4e2987b5ed84bf12b696e6024ae.svn-base ---------------------------------------------------------------------- diff --git a/site-content/.svn/pristine/02/025dd274e61ae4e2987b5ed84bf12b696e6024ae.svn-base b/site-content/.svn/pristine/02/025dd274e61ae4e2987b5ed84bf12b696e6024ae.svn-base deleted file mode 100644 index 5800518..0000000 --- a/site-content/.svn/pristine/02/025dd274e61ae4e2987b5ed84bf12b696e6024ae.svn-base +++ /dev/null @@ -1,335 +0,0 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd";> -<html lang="en"> -<head> -<title>Source code</title> -<link rel="stylesheet" type="text/css" href="../../../../../../../../stylesheet.css" title="Style"> -</head> -<body> -<div class="sourceContainer"> -<pre><span class="sourceLineNo">001</span>/*<a name="line.1"></a> -<span class="sourceLineNo">002</span> * Licensed to the Apache Software Foundation (ASF) under one or more<a name="line.2"></a> -<span class="sourceLineNo">003</span> * contributor license agreements. See the NOTICE file distributed with<a name="line.3"></a> -<span class="sourceLineNo">004</span> * this work for additional information regarding copyright ownership.<a name="line.4"></a> -<span class="sourceLineNo">005</span> * The ASF licenses this file to You under the Apache License, Version 2.0<a name="line.5"></a> -<span class="sourceLineNo">006</span> * (the "License"); you may not use this file except in compliance with<a name="line.6"></a> -<span class="sourceLineNo">007</span> * the License. You may obtain a copy of the License at<a name="line.7"></a> -<span class="sourceLineNo">008</span> *<a name="line.8"></a> -<span class="sourceLineNo">009</span> * http://www.apache.org/licenses/LICENSE-2.0<a name="line.9"></a> -<span class="sourceLineNo">010</span> *<a name="line.10"></a> -<span class="sourceLineNo">011</span> * Unless required by applicable law or agreed to in writing, software<a name="line.11"></a> -<span class="sourceLineNo">012</span> * distributed under the License is distributed on an "AS IS" BASIS,<a name="line.12"></a> -<span class="sourceLineNo">013</span> * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.<a name="line.13"></a> -<span class="sourceLineNo">014</span> * See the License for the specific language governing permissions and<a name="line.14"></a> -<span class="sourceLineNo">015</span> * limitations under the License.<a name="line.15"></a> -<span class="sourceLineNo">016</span> */<a name="line.16"></a> -<span class="sourceLineNo">017</span>package org.apache.commons.math3.geometry.euclidean.threed;<a name="line.17"></a> -<span class="sourceLineNo">018</span><a name="line.18"></a> -<span class="sourceLineNo">019</span>import java.util.ArrayList;<a name="line.19"></a> -<span class="sourceLineNo">020</span><a name="line.20"></a> -<span class="sourceLineNo">021</span>import org.apache.commons.math3.geometry.Point;<a name="line.21"></a> -<span class="sourceLineNo">022</span>import org.apache.commons.math3.geometry.euclidean.twod.Euclidean2D;<a name="line.22"></a> -<span class="sourceLineNo">023</span>import org.apache.commons.math3.geometry.euclidean.twod.PolygonsSet;<a name="line.23"></a> -<span class="sourceLineNo">024</span>import org.apache.commons.math3.geometry.euclidean.twod.Vector2D;<a name="line.24"></a> -<span class="sourceLineNo">025</span>import org.apache.commons.math3.geometry.partitioning.AbstractSubHyperplane;<a name="line.25"></a> -<span class="sourceLineNo">026</span>import org.apache.commons.math3.geometry.partitioning.BSPTree;<a name="line.26"></a> -<span class="sourceLineNo">027</span>import org.apache.commons.math3.geometry.partitioning.BSPTreeVisitor;<a name="line.27"></a> -<span class="sourceLineNo">028</span>import org.apache.commons.math3.geometry.partitioning.BoundaryAttribute;<a name="line.28"></a> -<span class="sourceLineNo">029</span>import org.apache.commons.math3.geometry.partitioning.RegionFactory;<a name="line.29"></a> -<span class="sourceLineNo">030</span>import org.apache.commons.math3.geometry.partitioning.SubHyperplane;<a name="line.30"></a> -<span class="sourceLineNo">031</span>import org.apache.commons.math3.util.FastMath;<a name="line.31"></a> -<span class="sourceLineNo">032</span><a name="line.32"></a> -<span class="sourceLineNo">033</span>/** Extractor for {@link PolygonsSet polyhedrons sets} outlines.<a name="line.33"></a> -<span class="sourceLineNo">034</span> * <p>This class extracts the 2D outlines from {{@link PolygonsSet<a name="line.34"></a> -<span class="sourceLineNo">035</span> * polyhedrons sets} in a specified projection plane.</p><a name="line.35"></a> -<span class="sourceLineNo">036</span> * @since 3.0<a name="line.36"></a> -<span class="sourceLineNo">037</span> */<a name="line.37"></a> -<span class="sourceLineNo">038</span>public class OutlineExtractor {<a name="line.38"></a> -<span class="sourceLineNo">039</span><a name="line.39"></a> -<span class="sourceLineNo">040</span> /** Abscissa axis of the projection plane. */<a name="line.40"></a> -<span class="sourceLineNo">041</span> private Vector3D u;<a name="line.41"></a> -<span class="sourceLineNo">042</span><a name="line.42"></a> -<span class="sourceLineNo">043</span> /** Ordinate axis of the projection plane. */<a name="line.43"></a> -<span class="sourceLineNo">044</span> private Vector3D v;<a name="line.44"></a> -<span class="sourceLineNo">045</span><a name="line.45"></a> -<span class="sourceLineNo">046</span> /** Normal of the projection plane (viewing direction). */<a name="line.46"></a> -<span class="sourceLineNo">047</span> private Vector3D w;<a name="line.47"></a> -<span class="sourceLineNo">048</span><a name="line.48"></a> -<span class="sourceLineNo">049</span> /** Build an extractor for a specific projection plane.<a name="line.49"></a> -<span class="sourceLineNo">050</span> * @param u abscissa axis of the projection point<a name="line.50"></a> -<span class="sourceLineNo">051</span> * @param v ordinate axis of the projection point<a name="line.51"></a> -<span class="sourceLineNo">052</span> */<a name="line.52"></a> -<span class="sourceLineNo">053</span> public OutlineExtractor(final Vector3D u, final Vector3D v) {<a name="line.53"></a> -<span class="sourceLineNo">054</span> this.u = u;<a name="line.54"></a> -<span class="sourceLineNo">055</span> this.v = v;<a name="line.55"></a> -<span class="sourceLineNo">056</span> w = Vector3D.crossProduct(u, v);<a name="line.56"></a> -<span class="sourceLineNo">057</span> }<a name="line.57"></a> -<span class="sourceLineNo">058</span><a name="line.58"></a> -<span class="sourceLineNo">059</span> /** Extract the outline of a polyhedrons set.<a name="line.59"></a> -<span class="sourceLineNo">060</span> * @param polyhedronsSet polyhedrons set whose outline must be extracted<a name="line.60"></a> -<span class="sourceLineNo">061</span> * @return an outline, as an array of loops.<a name="line.61"></a> -<span class="sourceLineNo">062</span> */<a name="line.62"></a> -<span class="sourceLineNo">063</span> public Vector2D[][] getOutline(final PolyhedronsSet polyhedronsSet) {<a name="line.63"></a> -<span class="sourceLineNo">064</span><a name="line.64"></a> -<span class="sourceLineNo">065</span> // project all boundary facets into one polygons set<a name="line.65"></a> -<span class="sourceLineNo">066</span> final BoundaryProjector projector = new BoundaryProjector(polyhedronsSet.getTolerance());<a name="line.66"></a> -<span class="sourceLineNo">067</span> polyhedronsSet.getTree(true).visit(projector);<a name="line.67"></a> -<span class="sourceLineNo">068</span> final PolygonsSet projected = projector.getProjected();<a name="line.68"></a> -<span class="sourceLineNo">069</span><a name="line.69"></a> -<span class="sourceLineNo">070</span> // Remove the spurious intermediate vertices from the outline<a name="line.70"></a> -<span class="sourceLineNo">071</span> final Vector2D[][] outline = projected.getVertices();<a name="line.71"></a> -<span class="sourceLineNo">072</span> for (int i = 0; i < outline.length; ++i) {<a name="line.72"></a> -<span class="sourceLineNo">073</span> final Vector2D[] rawLoop = outline[i];<a name="line.73"></a> -<span class="sourceLineNo">074</span> int end = rawLoop.length;<a name="line.74"></a> -<span class="sourceLineNo">075</span> int j = 0;<a name="line.75"></a> -<span class="sourceLineNo">076</span> while (j < end) {<a name="line.76"></a> -<span class="sourceLineNo">077</span> if (pointIsBetween(rawLoop, end, j)) {<a name="line.77"></a> -<span class="sourceLineNo">078</span> // the point should be removed<a name="line.78"></a> -<span class="sourceLineNo">079</span> for (int k = j; k < (end - 1); ++k) {<a name="line.79"></a> -<span class="sourceLineNo">080</span> rawLoop[k] = rawLoop[k + 1];<a name="line.80"></a> -<span class="sourceLineNo">081</span> }<a name="line.81"></a> -<span class="sourceLineNo">082</span> --end;<a name="line.82"></a> -<span class="sourceLineNo">083</span> } else {<a name="line.83"></a> -<span class="sourceLineNo">084</span> // the point remains in the loop<a name="line.84"></a> -<span class="sourceLineNo">085</span> ++j;<a name="line.85"></a> -<span class="sourceLineNo">086</span> }<a name="line.86"></a> -<span class="sourceLineNo">087</span> }<a name="line.87"></a> -<span class="sourceLineNo">088</span> if (end != rawLoop.length) {<a name="line.88"></a> -<span class="sourceLineNo">089</span> // resize the array<a name="line.89"></a> -<span class="sourceLineNo">090</span> outline[i] = new Vector2D[end];<a name="line.90"></a> -<span class="sourceLineNo">091</span> System.arraycopy(rawLoop, 0, outline[i], 0, end);<a name="line.91"></a> -<span class="sourceLineNo">092</span> }<a name="line.92"></a> -<span class="sourceLineNo">093</span> }<a name="line.93"></a> -<span class="sourceLineNo">094</span><a name="line.94"></a> -<span class="sourceLineNo">095</span> return outline;<a name="line.95"></a> -<span class="sourceLineNo">096</span><a name="line.96"></a> -<span class="sourceLineNo">097</span> }<a name="line.97"></a> -<span class="sourceLineNo">098</span><a name="line.98"></a> -<span class="sourceLineNo">099</span> /** Check if a point is geometrically between its neighbor in an array.<a name="line.99"></a> -<span class="sourceLineNo">100</span> * <p>The neighbors are computed considering the array is a loop<a name="line.100"></a> -<span class="sourceLineNo">101</span> * (i.e. point at index (n-1) is before point at index 0)</p><a name="line.101"></a> -<span class="sourceLineNo">102</span> * @param loop points array<a name="line.102"></a> -<span class="sourceLineNo">103</span> * @param n number of points to consider in the array<a name="line.103"></a> -<span class="sourceLineNo">104</span> * @param i index of the point to check (must be between 0 and n-1)<a name="line.104"></a> -<span class="sourceLineNo">105</span> * @return true if the point is exactly between its neighbors<a name="line.105"></a> -<span class="sourceLineNo">106</span> */<a name="line.106"></a> -<span class="sourceLineNo">107</span> private boolean pointIsBetween(final Vector2D[] loop, final int n, final int i) {<a name="line.107"></a> -<span class="sourceLineNo">108</span> final Vector2D previous = loop[(i + n - 1) % n];<a name="line.108"></a> -<span class="sourceLineNo">109</span> final Vector2D current = loop[i];<a name="line.109"></a> -<span class="sourceLineNo">110</span> final Vector2D next = loop[(i + 1) % n];<a name="line.110"></a> -<span class="sourceLineNo">111</span> final double dx1 = current.getX() - previous.getX();<a name="line.111"></a> -<span class="sourceLineNo">112</span> final double dy1 = current.getY() - previous.getY();<a name="line.112"></a> -<span class="sourceLineNo">113</span> final double dx2 = next.getX() - current.getX();<a name="line.113"></a> -<span class="sourceLineNo">114</span> final double dy2 = next.getY() - current.getY();<a name="line.114"></a> -<span class="sourceLineNo">115</span> final double cross = dx1 * dy2 - dx2 * dy1;<a name="line.115"></a> -<span class="sourceLineNo">116</span> final double dot = dx1 * dx2 + dy1 * dy2;<a name="line.116"></a> -<span class="sourceLineNo">117</span> final double d1d2 = FastMath.sqrt((dx1 * dx1 + dy1 * dy1) * (dx2 * dx2 + dy2 * dy2));<a name="line.117"></a> -<span class="sourceLineNo">118</span> return (FastMath.abs(cross) <= (1.0e-6 * d1d2)) && (dot >= 0.0);<a name="line.118"></a> -<span class="sourceLineNo">119</span> }<a name="line.119"></a> -<span class="sourceLineNo">120</span><a name="line.120"></a> -<span class="sourceLineNo">121</span> /** Visitor projecting the boundary facets on a plane. */<a name="line.121"></a> -<span class="sourceLineNo">122</span> private class BoundaryProjector implements BSPTreeVisitor<Euclidean3D> {<a name="line.122"></a> -<span class="sourceLineNo">123</span><a name="line.123"></a> -<span class="sourceLineNo">124</span> /** Projection of the polyhedrons set on the plane. */<a name="line.124"></a> -<span class="sourceLineNo">125</span> private PolygonsSet projected;<a name="line.125"></a> -<span class="sourceLineNo">126</span><a name="line.126"></a> -<span class="sourceLineNo">127</span> /** Tolerance below which points are considered identical. */<a name="line.127"></a> -<span class="sourceLineNo">128</span> private final double tolerance;<a name="line.128"></a> -<span class="sourceLineNo">129</span><a name="line.129"></a> -<span class="sourceLineNo">130</span> /** Simple constructor.<a name="line.130"></a> -<span class="sourceLineNo">131</span> * @param tolerance tolerance below which points are considered identical<a name="line.131"></a> -<span class="sourceLineNo">132</span> */<a name="line.132"></a> -<span class="sourceLineNo">133</span> BoundaryProjector(final double tolerance) {<a name="line.133"></a> -<span class="sourceLineNo">134</span> this.projected = new PolygonsSet(new BSPTree<Euclidean2D>(Boolean.FALSE), tolerance);<a name="line.134"></a> -<span class="sourceLineNo">135</span> this.tolerance = tolerance;<a name="line.135"></a> -<span class="sourceLineNo">136</span> }<a name="line.136"></a> -<span class="sourceLineNo">137</span><a name="line.137"></a> -<span class="sourceLineNo">138</span> /** {@inheritDoc} */<a name="line.138"></a> -<span class="sourceLineNo">139</span> public Order visitOrder(final BSPTree<Euclidean3D> node) {<a name="line.139"></a> -<span class="sourceLineNo">140</span> return Order.MINUS_SUB_PLUS;<a name="line.140"></a> -<span class="sourceLineNo">141</span> }<a name="line.141"></a> -<span class="sourceLineNo">142</span><a name="line.142"></a> -<span class="sourceLineNo">143</span> /** {@inheritDoc} */<a name="line.143"></a> -<span class="sourceLineNo">144</span> public void visitInternalNode(final BSPTree<Euclidean3D> node) {<a name="line.144"></a> -<span class="sourceLineNo">145</span> @SuppressWarnings("unchecked")<a name="line.145"></a> -<span class="sourceLineNo">146</span> final BoundaryAttribute<Euclidean3D> attribute =<a name="line.146"></a> -<span class="sourceLineNo">147</span> (BoundaryAttribute<Euclidean3D>) node.getAttribute();<a name="line.147"></a> -<span class="sourceLineNo">148</span> if (attribute.getPlusOutside() != null) {<a name="line.148"></a> -<span class="sourceLineNo">149</span> addContribution(attribute.getPlusOutside(), false);<a name="line.149"></a> -<span class="sourceLineNo">150</span> }<a name="line.150"></a> -<span class="sourceLineNo">151</span> if (attribute.getPlusInside() != null) {<a name="line.151"></a> -<span class="sourceLineNo">152</span> addContribution(attribute.getPlusInside(), true);<a name="line.152"></a> -<span class="sourceLineNo">153</span> }<a name="line.153"></a> -<span class="sourceLineNo">154</span> }<a name="line.154"></a> -<span class="sourceLineNo">155</span><a name="line.155"></a> -<span class="sourceLineNo">156</span> /** {@inheritDoc} */<a name="line.156"></a> -<span class="sourceLineNo">157</span> public void visitLeafNode(final BSPTree<Euclidean3D> node) {<a name="line.157"></a> -<span class="sourceLineNo">158</span> }<a name="line.158"></a> -<span class="sourceLineNo">159</span><a name="line.159"></a> -<span class="sourceLineNo">160</span> /** Add he contribution of a boundary facet.<a name="line.160"></a> -<span class="sourceLineNo">161</span> * @param facet boundary facet<a name="line.161"></a> -<span class="sourceLineNo">162</span> * @param reversed if true, the facet has the inside on its plus side<a name="line.162"></a> -<span class="sourceLineNo">163</span> */<a name="line.163"></a> -<span class="sourceLineNo">164</span> private void addContribution(final SubHyperplane<Euclidean3D> facet, final boolean reversed) {<a name="line.164"></a> -<span class="sourceLineNo">165</span><a name="line.165"></a> -<span class="sourceLineNo">166</span> // extract the vertices of the facet<a name="line.166"></a> -<span class="sourceLineNo">167</span> @SuppressWarnings("unchecked")<a name="line.167"></a> -<span class="sourceLineNo">168</span> final AbstractSubHyperplane<Euclidean3D, Euclidean2D> absFacet =<a name="line.168"></a> -<span class="sourceLineNo">169</span> (AbstractSubHyperplane<Euclidean3D, Euclidean2D>) facet;<a name="line.169"></a> -<span class="sourceLineNo">170</span> final Plane plane = (Plane) facet.getHyperplane();<a name="line.170"></a> -<span class="sourceLineNo">171</span><a name="line.171"></a> -<span class="sourceLineNo">172</span> final double scal = plane.getNormal().dotProduct(w);<a name="line.172"></a> -<span class="sourceLineNo">173</span> if (FastMath.abs(scal) > 1.0e-3) {<a name="line.173"></a> -<span class="sourceLineNo">174</span> Vector2D[][] vertices =<a name="line.174"></a> -<span class="sourceLineNo">175</span> ((PolygonsSet) absFacet.getRemainingRegion()).getVertices();<a name="line.175"></a> -<span class="sourceLineNo">176</span><a name="line.176"></a> -<span class="sourceLineNo">177</span> if ((scal < 0) ^ reversed) {<a name="line.177"></a> -<span class="sourceLineNo">178</span> // the facet is seen from the inside,<a name="line.178"></a> -<span class="sourceLineNo">179</span> // we need to invert its boundary orientation<a name="line.179"></a> -<span class="sourceLineNo">180</span> final Vector2D[][] newVertices = new Vector2D[vertices.length][];<a name="line.180"></a> -<span class="sourceLineNo">181</span> for (int i = 0; i < vertices.length; ++i) {<a name="line.181"></a> -<span class="sourceLineNo">182</span> final Vector2D[] loop = vertices[i];<a name="line.182"></a> -<span class="sourceLineNo">183</span> final Vector2D[] newLoop = new Vector2D[loop.length];<a name="line.183"></a> -<span class="sourceLineNo">184</span> if (loop[0] == null) {<a name="line.184"></a> -<span class="sourceLineNo">185</span> newLoop[0] = null;<a name="line.185"></a> -<span class="sourceLineNo">186</span> for (int j = 1; j < loop.length; ++j) {<a name="line.186"></a> -<span class="sourceLineNo">187</span> newLoop[j] = loop[loop.length - j];<a name="line.187"></a> -<span class="sourceLineNo">188</span> }<a name="line.188"></a> -<span class="sourceLineNo">189</span> } else {<a name="line.189"></a> -<span class="sourceLineNo">190</span> for (int j = 0; j < loop.length; ++j) {<a name="line.190"></a> -<span class="sourceLineNo">191</span> newLoop[j] = loop[loop.length - (j + 1)];<a name="line.191"></a> -<span class="sourceLineNo">192</span> }<a name="line.192"></a> -<span class="sourceLineNo">193</span> }<a name="line.193"></a> -<span class="sourceLineNo">194</span> newVertices[i] = newLoop;<a name="line.194"></a> -<span class="sourceLineNo">195</span> }<a name="line.195"></a> -<span class="sourceLineNo">196</span><a name="line.196"></a> -<span class="sourceLineNo">197</span> // use the reverted vertices<a name="line.197"></a> -<span class="sourceLineNo">198</span> vertices = newVertices;<a name="line.198"></a> -<span class="sourceLineNo">199</span><a name="line.199"></a> -<span class="sourceLineNo">200</span> }<a name="line.200"></a> -<span class="sourceLineNo">201</span><a name="line.201"></a> -<span class="sourceLineNo">202</span> // compute the projection of the facet in the outline plane<a name="line.202"></a> -<span class="sourceLineNo">203</span> final ArrayList<SubHyperplane<Euclidean2D>> edges = new ArrayList<SubHyperplane<Euclidean2D>>();<a name="line.203"></a> -<span class="sourceLineNo">204</span> for (Vector2D[] loop : vertices) {<a name="line.204"></a> -<span class="sourceLineNo">205</span> final boolean closed = loop[0] != null;<a name="line.205"></a> -<span class="sourceLineNo">206</span> int previous = closed ? (loop.length - 1) : 1;<a name="line.206"></a> -<span class="sourceLineNo">207</span> Vector3D previous3D = plane.toSpace((Point<Euclidean2D>) loop[previous]);<a name="line.207"></a> -<span class="sourceLineNo">208</span> int current = (previous + 1) % loop.length;<a name="line.208"></a> -<span class="sourceLineNo">209</span> Vector2D pPoint = new Vector2D(previous3D.dotProduct(u),<a name="line.209"></a> -<span class="sourceLineNo">210</span> previous3D.dotProduct(v));<a name="line.210"></a> -<span class="sourceLineNo">211</span> while (current < loop.length) {<a name="line.211"></a> -<span class="sourceLineNo">212</span><a name="line.212"></a> -<span class="sourceLineNo">213</span> final Vector3D current3D = plane.toSpace((Point<Euclidean2D>) loop[current]);<a name="line.213"></a> -<span class="sourceLineNo">214</span> final Vector2D cPoint = new Vector2D(current3D.dotProduct(u),<a name="line.214"></a> -<span class="sourceLineNo">215</span> current3D.dotProduct(v));<a name="line.215"></a> -<span class="sourceLineNo">216</span> final org.apache.commons.math3.geometry.euclidean.twod.Line line =<a name="line.216"></a> -<span class="sourceLineNo">217</span> new org.apache.commons.math3.geometry.euclidean.twod.Line(pPoint, cPoint, tolerance);<a name="line.217"></a> -<span class="sourceLineNo">218</span> SubHyperplane<Euclidean2D> edge = line.wholeHyperplane();<a name="line.218"></a> -<span class="sourceLineNo">219</span><a name="line.219"></a> -<span class="sourceLineNo">220</span> if (closed || (previous != 1)) {<a name="line.220"></a> -<span class="sourceLineNo">221</span> // the previous point is a real vertex<a name="line.221"></a> -<span class="sourceLineNo">222</span> // it defines one bounding point of the edge<a name="line.222"></a> -<span class="sourceLineNo">223</span> final double angle = line.getAngle() + 0.5 * FastMath.PI;<a name="line.223"></a> -<span class="sourceLineNo">224</span> final org.apache.commons.math3.geometry.euclidean.twod.Line l =<a name="line.224"></a> -<span class="sourceLineNo">225</span> new org.apache.commons.math3.geometry.euclidean.twod.Line(pPoint, angle, tolerance);<a name="line.225"></a> -<span class="sourceLineNo">226</span> edge = edge.split(l).getPlus();<a name="line.226"></a> -<span class="sourceLineNo">227</span> }<a name="line.227"></a> -<span class="sourceLineNo">228</span><a name="line.228"></a> -<span class="sourceLineNo">229</span> if (closed || (current != (loop.length - 1))) {<a name="line.229"></a> -<span class="sourceLineNo">230</span> // the current point is a real vertex<a name="line.230"></a> -<span class="sourceLineNo">231</span> // it defines one bounding point of the edge<a name="line.231"></a> -<span class="sourceLineNo">232</span> final double angle = line.getAngle() + 0.5 * FastMath.PI;<a name="line.232"></a> -<span class="sourceLineNo">233</span> final org.apache.commons.math3.geometry.euclidean.twod.Line l =<a name="line.233"></a> -<span class="sourceLineNo">234</span> new org.apache.commons.math3.geometry.euclidean.twod.Line(cPoint, angle, tolerance);<a name="line.234"></a> -<span class="sourceLineNo">235</span> edge = edge.split(l).getMinus();<a name="line.235"></a> -<span class="sourceLineNo">236</span> }<a name="line.236"></a> -<span class="sourceLineNo">237</span><a name="line.237"></a> -<span class="sourceLineNo">238</span> edges.add(edge);<a name="line.238"></a> -<span class="sourceLineNo">239</span><a name="line.239"></a> -<span class="sourceLineNo">240</span> previous = current++;<a name="line.240"></a> -<span class="sourceLineNo">241</span> previous3D = current3D;<a name="line.241"></a> -<span class="sourceLineNo">242</span> pPoint = cPoint;<a name="line.242"></a> -<span class="sourceLineNo">243</span><a name="line.243"></a> -<span class="sourceLineNo">244</span> }<a name="line.244"></a> -<span class="sourceLineNo">245</span> }<a name="line.245"></a> -<span class="sourceLineNo">246</span> final PolygonsSet projectedFacet = new PolygonsSet(edges, tolerance);<a name="line.246"></a> -<span class="sourceLineNo">247</span><a name="line.247"></a> -<span class="sourceLineNo">248</span> // add the contribution of the facet to the global outline<a name="line.248"></a> -<span class="sourceLineNo">249</span> projected = (PolygonsSet) new RegionFactory<Euclidean2D>().union(projected, projectedFacet);<a name="line.249"></a> -<span class="sourceLineNo">250</span><a name="line.250"></a> -<span class="sourceLineNo">251</span> }<a name="line.251"></a> -<span class="sourceLineNo">252</span> }<a name="line.252"></a> -<span class="sourceLineNo">253</span><a name="line.253"></a> -<span class="sourceLineNo">254</span> /** Get the projection of the polyhedrons set on the plane.<a name="line.254"></a> -<span class="sourceLineNo">255</span> * @return projection of the polyhedrons set on the plane<a name="line.255"></a> -<span class="sourceLineNo">256</span> */<a name="line.256"></a> -<span class="sourceLineNo">257</span> public PolygonsSet getProjected() {<a name="line.257"></a> -<span class="sourceLineNo">258</span> return projected;<a name="line.258"></a> -<span class="sourceLineNo">259</span> }<a name="line.259"></a> -<span class="sourceLineNo">260</span><a name="line.260"></a> -<span class="sourceLineNo">261</span> }<a name="line.261"></a> -<span class="sourceLineNo">262</span><a name="line.262"></a> -<span class="sourceLineNo">263</span>}<a name="line.263"></a> - 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