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| <pre><span class="sourceLineNo">001</span>/*-<a name="line.1"></a> |
| <span class="sourceLineNo">002</span> *******************************************************************************<a name="line.2"></a> |
| <span class="sourceLineNo">003</span> * Copyright (c) 2011, 2016 Diamond Light Source Ltd.<a name="line.3"></a> |
| <span class="sourceLineNo">004</span> * All rights reserved. This program and the accompanying materials<a name="line.4"></a> |
| <span class="sourceLineNo">005</span> * are made available under the terms of the Eclipse Public License v1.0<a name="line.5"></a> |
| <span class="sourceLineNo">006</span> * which accompanies this distribution, and is available at<a name="line.6"></a> |
| <span class="sourceLineNo">007</span> * http://www.eclipse.org/legal/epl-v10.html<a name="line.7"></a> |
| <span class="sourceLineNo">008</span> *<a name="line.8"></a> |
| <span class="sourceLineNo">009</span> * Contributors:<a name="line.9"></a> |
| <span class="sourceLineNo">010</span> * Peter Chang - initial API and implementation and/or initial documentation<a name="line.10"></a> |
| <span class="sourceLineNo">011</span> *******************************************************************************/<a name="line.11"></a> |
| <span class="sourceLineNo">012</span><a name="line.12"></a> |
| <span class="sourceLineNo">013</span>package org.eclipse.january.dataset;<a name="line.13"></a> |
| <span class="sourceLineNo">014</span><a name="line.14"></a> |
| <span class="sourceLineNo">015</span>import java.io.IOException;<a name="line.15"></a> |
| <span class="sourceLineNo">016</span>import java.io.Serializable;<a name="line.16"></a> |
| <span class="sourceLineNo">017</span>import java.lang.annotation.Annotation;<a name="line.17"></a> |
| <span class="sourceLineNo">018</span>import java.lang.reflect.Field;<a name="line.18"></a> |
| <span class="sourceLineNo">019</span>import java.util.ArrayList;<a name="line.19"></a> |
| <span class="sourceLineNo">020</span>import java.util.Arrays;<a name="line.20"></a> |
| <span class="sourceLineNo">021</span>import java.util.HashMap;<a name="line.21"></a> |
| <span class="sourceLineNo">022</span>import java.util.LinkedList;<a name="line.22"></a> |
| <span class="sourceLineNo">023</span>import java.util.List;<a name="line.23"></a> |
| <span class="sourceLineNo">024</span>import java.util.Map;<a name="line.24"></a> |
| <span class="sourceLineNo">025</span><a name="line.25"></a> |
| <span class="sourceLineNo">026</span>import org.eclipse.january.DatasetException;<a name="line.26"></a> |
| <span class="sourceLineNo">027</span>import org.eclipse.january.IMonitor;<a name="line.27"></a> |
| <span class="sourceLineNo">028</span>import org.eclipse.january.io.ILazyLoader;<a name="line.28"></a> |
| <span class="sourceLineNo">029</span>import org.eclipse.january.metadata.MetadataFactory;<a name="line.29"></a> |
| <span class="sourceLineNo">030</span>import org.eclipse.january.metadata.MetadataType;<a name="line.30"></a> |
| <span class="sourceLineNo">031</span>import org.eclipse.january.metadata.OriginMetadata;<a name="line.31"></a> |
| <span class="sourceLineNo">032</span>import org.eclipse.january.metadata.Reshapeable;<a name="line.32"></a> |
| <span class="sourceLineNo">033</span>import org.eclipse.january.metadata.Sliceable;<a name="line.33"></a> |
| <span class="sourceLineNo">034</span>import org.eclipse.january.metadata.Transposable;<a name="line.34"></a> |
| <span class="sourceLineNo">035</span><a name="line.35"></a> |
| <span class="sourceLineNo">036</span>public class LazyDataset extends LazyDatasetBase implements Serializable, Cloneable {<a name="line.36"></a> |
| <span class="sourceLineNo">037</span> private static final long serialVersionUID = 2467865859867440242L;<a name="line.37"></a> |
| <span class="sourceLineNo">038</span><a name="line.38"></a> |
| <span class="sourceLineNo">039</span> protected Map<Class<? extends MetadataType>, List<MetadataType>> oMetadata = null;<a name="line.39"></a> |
| <span class="sourceLineNo">040</span> protected int[] oShape; // original shape<a name="line.40"></a> |
| <span class="sourceLineNo">041</span> protected long size; // number of items<a name="line.41"></a> |
| <span class="sourceLineNo">042</span> private Class<? extends Dataset> clazz = null;<a name="line.42"></a> |
| <span class="sourceLineNo">043</span> protected int isize; // number of elements per item<a name="line.43"></a> |
| <span class="sourceLineNo">044</span><a name="line.44"></a> |
| <span class="sourceLineNo">045</span> protected ILazyLoader loader;<a name="line.45"></a> |
| <span class="sourceLineNo">046</span><a name="line.46"></a> |
| <span class="sourceLineNo">047</span> // relative to loader<a name="line.47"></a> |
| <span class="sourceLineNo">048</span> protected int[] begSlice = null; // slice begin<a name="line.48"></a> |
| <span class="sourceLineNo">049</span> protected int[] delSlice = null; // slice delta<a name="line.49"></a> |
| <span class="sourceLineNo">050</span> /**<a name="line.50"></a> |
| <span class="sourceLineNo">051</span> * @since 2.2<a name="line.51"></a> |
| <span class="sourceLineNo">052</span> */<a name="line.52"></a> |
| <span class="sourceLineNo">053</span> protected int[] sShape = null; // sliced shape<a name="line.53"></a> |
| <span class="sourceLineNo">054</span><a name="line.54"></a> |
| <span class="sourceLineNo">055</span> /**<a name="line.55"></a> |
| <span class="sourceLineNo">056</span> * @since 2.2<a name="line.56"></a> |
| <span class="sourceLineNo">057</span> */<a name="line.57"></a> |
| <span class="sourceLineNo">058</span> protected int[] padding = null; // differences in shape from original (or sliced) shape<a name="line.58"></a> |
| <span class="sourceLineNo">059</span> protected int[] map; // transposition map (same length as current shape)<a name="line.59"></a> |
| <span class="sourceLineNo">060</span><a name="line.60"></a> |
| <span class="sourceLineNo">061</span> /**<a name="line.61"></a> |
| <span class="sourceLineNo">062</span> * Create a lazy dataset<a name="line.62"></a> |
| <span class="sourceLineNo">063</span> * @param loader<a name="line.63"></a> |
| <span class="sourceLineNo">064</span> * @param name<a name="line.64"></a> |
| <span class="sourceLineNo">065</span> * @param elements<a name="line.65"></a> |
| <span class="sourceLineNo">066</span> * @param clazz dataset interface<a name="line.66"></a> |
| <span class="sourceLineNo">067</span> * @param shape<a name="line.67"></a> |
| <span class="sourceLineNo">068</span> * @since 2.3<a name="line.68"></a> |
| <span class="sourceLineNo">069</span> */<a name="line.69"></a> |
| <span class="sourceLineNo">070</span> public LazyDataset(ILazyLoader loader, String name, int elements, Class<? extends Dataset> clazz, int... shape) {<a name="line.70"></a> |
| <span class="sourceLineNo">071</span> this.loader = loader;<a name="line.71"></a> |
| <span class="sourceLineNo">072</span> this.name = name;<a name="line.72"></a> |
| <span class="sourceLineNo">073</span> this.isize = elements;<a name="line.73"></a> |
| <span class="sourceLineNo">074</span> this.clazz = clazz;<a name="line.74"></a> |
| <span class="sourceLineNo">075</span> this.shape = shape.clone();<a name="line.75"></a> |
| <span class="sourceLineNo">076</span> this.oShape = this.shape;<a name="line.76"></a> |
| <span class="sourceLineNo">077</span> try {<a name="line.77"></a> |
| <span class="sourceLineNo">078</span> size = ShapeUtils.calcLongSize(shape);<a name="line.78"></a> |
| <span class="sourceLineNo">079</span> } catch (IllegalArgumentException e) {<a name="line.79"></a> |
| <span class="sourceLineNo">080</span> size = Long.MAX_VALUE; // this indicates that the entire dataset cannot be read in! <a name="line.80"></a> |
| <span class="sourceLineNo">081</span> }<a name="line.81"></a> |
| <span class="sourceLineNo">082</span> }<a name="line.82"></a> |
| <span class="sourceLineNo">083</span><a name="line.83"></a> |
| <span class="sourceLineNo">084</span> /**<a name="line.84"></a> |
| <span class="sourceLineNo">085</span> * Create a lazy dataset<a name="line.85"></a> |
| <span class="sourceLineNo">086</span> * @param loader<a name="line.86"></a> |
| <span class="sourceLineNo">087</span> * @param name<a name="line.87"></a> |
| <span class="sourceLineNo">088</span> * @param clazz dataset interface<a name="line.88"></a> |
| <span class="sourceLineNo">089</span> * @param shape<a name="line.89"></a> |
| <span class="sourceLineNo">090</span> * @since 2.3<a name="line.90"></a> |
| <span class="sourceLineNo">091</span> */<a name="line.91"></a> |
| <span class="sourceLineNo">092</span> public LazyDataset(ILazyLoader loader, String name, Class<? extends Dataset> clazz, int... shape) {<a name="line.92"></a> |
| <span class="sourceLineNo">093</span> this(loader, name, 1, clazz, shape);<a name="line.93"></a> |
| <span class="sourceLineNo">094</span> }<a name="line.94"></a> |
| <span class="sourceLineNo">095</span><a name="line.95"></a> |
| <span class="sourceLineNo">096</span> /**<a name="line.96"></a> |
| <span class="sourceLineNo">097</span> * Create a lazy dataset<a name="line.97"></a> |
| <span class="sourceLineNo">098</span> * @param name<a name="line.98"></a> |
| <span class="sourceLineNo">099</span> * @param dtype dataset type<a name="line.99"></a> |
| <span class="sourceLineNo">100</span> * @param elements<a name="line.100"></a> |
| <span class="sourceLineNo">101</span> * @param shape<a name="line.101"></a> |
| <span class="sourceLineNo">102</span> * @param loader<a name="line.102"></a> |
| <span class="sourceLineNo">103</span> * @deprecated Use {@link #LazyDataset(ILazyLoader, String, int, Class, int[])}<a name="line.103"></a> |
| <span class="sourceLineNo">104</span> */<a name="line.104"></a> |
| <span class="sourceLineNo">105</span> @Deprecated<a name="line.105"></a> |
| <span class="sourceLineNo">106</span> public LazyDataset(String name, int dtype, int elements, int[] shape, ILazyLoader loader) {<a name="line.106"></a> |
| <span class="sourceLineNo">107</span> this(loader, name, elements, DTypeUtils.getInterface(dtype), shape);<a name="line.107"></a> |
| <span class="sourceLineNo">108</span> }<a name="line.108"></a> |
| <span class="sourceLineNo">109</span><a name="line.109"></a> |
| <span class="sourceLineNo">110</span> /**<a name="line.110"></a> |
| <span class="sourceLineNo">111</span> * Create a lazy dataset<a name="line.111"></a> |
| <span class="sourceLineNo">112</span> * @param name<a name="line.112"></a> |
| <span class="sourceLineNo">113</span> * @param dtype dataset type<a name="line.113"></a> |
| <span class="sourceLineNo">114</span> * @param shape<a name="line.114"></a> |
| <span class="sourceLineNo">115</span> * @param loader<a name="line.115"></a> |
| <span class="sourceLineNo">116</span> * @deprecated Use {@link #LazyDataset(ILazyLoader, String, int, Class, int[])}<a name="line.116"></a> |
| <span class="sourceLineNo">117</span> */<a name="line.117"></a> |
| <span class="sourceLineNo">118</span> @Deprecated<a name="line.118"></a> |
| <span class="sourceLineNo">119</span> public LazyDataset(String name, int dtype, int[] shape, ILazyLoader loader) {<a name="line.119"></a> |
| <span class="sourceLineNo">120</span> this(name, dtype, 1, shape, loader);<a name="line.120"></a> |
| <span class="sourceLineNo">121</span> }<a name="line.121"></a> |
| <span class="sourceLineNo">122</span><a name="line.122"></a> |
| <span class="sourceLineNo">123</span> LazyDataset(LazyDataset other) {<a name="line.123"></a> |
| <span class="sourceLineNo">124</span> name = other.name;<a name="line.124"></a> |
| <span class="sourceLineNo">125</span> shape = other.shape.clone();<a name="line.125"></a> |
| <span class="sourceLineNo">126</span> metadata = other.copyMetadata();<a name="line.126"></a> |
| <span class="sourceLineNo">127</span> oMetadata = other.oMetadata;<a name="line.127"></a> |
| <span class="sourceLineNo">128</span> oShape = other.oShape;<a name="line.128"></a> |
| <span class="sourceLineNo">129</span> size = other.size;<a name="line.129"></a> |
| <span class="sourceLineNo">130</span> clazz = other.clazz;<a name="line.130"></a> |
| <span class="sourceLineNo">131</span> isize = other.isize;<a name="line.131"></a> |
| <span class="sourceLineNo">132</span> loader = other.loader;<a name="line.132"></a> |
| <span class="sourceLineNo">133</span><a name="line.133"></a> |
| <span class="sourceLineNo">134</span> begSlice = other.begSlice;<a name="line.134"></a> |
| <span class="sourceLineNo">135</span> delSlice = other.delSlice;<a name="line.135"></a> |
| <span class="sourceLineNo">136</span> sShape = other.sShape;<a name="line.136"></a> |
| <span class="sourceLineNo">137</span> padding = other.padding;<a name="line.137"></a> |
| <span class="sourceLineNo">138</span> map = other.map;<a name="line.138"></a> |
| <span class="sourceLineNo">139</span> }<a name="line.139"></a> |
| <span class="sourceLineNo">140</span><a name="line.140"></a> |
| <span class="sourceLineNo">141</span> /**<a name="line.141"></a> |
| <span class="sourceLineNo">142</span> * Create a lazy dataset based on in-memory data (handy for testing)<a name="line.142"></a> |
| <span class="sourceLineNo">143</span> * @param dataset<a name="line.143"></a> |
| <span class="sourceLineNo">144</span> */<a name="line.144"></a> |
| <span class="sourceLineNo">145</span> public static LazyDataset createLazyDataset(final Dataset dataset) {<a name="line.145"></a> |
| <span class="sourceLineNo">146</span> return new LazyDataset(dataset.getName(), dataset.getDType(), dataset.getElementsPerItem(), dataset.getShapeRef(),<a name="line.146"></a> |
| <span class="sourceLineNo">147</span> new ILazyLoader() {<a name="line.147"></a> |
| <span class="sourceLineNo">148</span> private static final long serialVersionUID = -6725268922780517523L;<a name="line.148"></a> |
| <span class="sourceLineNo">149</span><a name="line.149"></a> |
| <span class="sourceLineNo">150</span> final Dataset d = dataset;<a name="line.150"></a> |
| <span class="sourceLineNo">151</span> @Override<a name="line.151"></a> |
| <span class="sourceLineNo">152</span> public boolean isFileReadable() {<a name="line.152"></a> |
| <span class="sourceLineNo">153</span> return true;<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> @Override<a name="line.156"></a> |
| <span class="sourceLineNo">157</span> public Dataset getDataset(IMonitor mon, SliceND slice) throws IOException {<a name="line.157"></a> |
| <span class="sourceLineNo">158</span> return d.getSlice(mon, slice);<a name="line.158"></a> |
| <span class="sourceLineNo">159</span> }<a name="line.159"></a> |
| <span class="sourceLineNo">160</span> });<a name="line.160"></a> |
| <span class="sourceLineNo">161</span> }<a name="line.161"></a> |
| <span class="sourceLineNo">162</span><a name="line.162"></a> |
| <span class="sourceLineNo">163</span> /**<a name="line.163"></a> |
| <span class="sourceLineNo">164</span> * Can return -1 for unknown<a name="line.164"></a> |
| <span class="sourceLineNo">165</span> */<a name="line.165"></a> |
| <span class="sourceLineNo">166</span> @Override<a name="line.166"></a> |
| <span class="sourceLineNo">167</span> public int getDType() {<a name="line.167"></a> |
| <span class="sourceLineNo">168</span> return DTypeUtils.getDType(clazz);<a name="line.168"></a> |
| <span class="sourceLineNo">169</span> }<a name="line.169"></a> |
| <span class="sourceLineNo">170</span><a name="line.170"></a> |
| <span class="sourceLineNo">171</span> /**<a name="line.171"></a> |
| <span class="sourceLineNo">172</span> * @return dataset interface that supports element class and number of elements<a name="line.172"></a> |
| <span class="sourceLineNo">173</span> * @since 2.3<a name="line.173"></a> |
| <span class="sourceLineNo">174</span> */<a name="line.174"></a> |
| <span class="sourceLineNo">175</span> public Class<? extends Dataset> getInterface() {<a name="line.175"></a> |
| <span class="sourceLineNo">176</span> return clazz;<a name="line.176"></a> |
| <span class="sourceLineNo">177</span> }<a name="line.177"></a> |
| <span class="sourceLineNo">178</span><a name="line.178"></a> |
| <span class="sourceLineNo">179</span> /**<a name="line.179"></a> |
| <span class="sourceLineNo">180</span> * Can return -1 for unknown<a name="line.180"></a> |
| <span class="sourceLineNo">181</span> */<a name="line.181"></a> |
| <span class="sourceLineNo">182</span> @Override<a name="line.182"></a> |
| <span class="sourceLineNo">183</span> public int getElementsPerItem() {<a name="line.183"></a> |
| <span class="sourceLineNo">184</span> return isize;<a name="line.184"></a> |
| <span class="sourceLineNo">185</span> }<a name="line.185"></a> |
| <span class="sourceLineNo">186</span><a name="line.186"></a> |
| <span class="sourceLineNo">187</span> @Override<a name="line.187"></a> |
| <span class="sourceLineNo">188</span> public int getSize() {<a name="line.188"></a> |
| <span class="sourceLineNo">189</span> return (int) size;<a name="line.189"></a> |
| <span class="sourceLineNo">190</span> }<a name="line.190"></a> |
| <span class="sourceLineNo">191</span><a name="line.191"></a> |
| <span class="sourceLineNo">192</span> @Override<a name="line.192"></a> |
| <span class="sourceLineNo">193</span> public String toString() {<a name="line.193"></a> |
| <span class="sourceLineNo">194</span> StringBuilder out = new StringBuilder();<a name="line.194"></a> |
| <span class="sourceLineNo">195</span><a name="line.195"></a> |
| <span class="sourceLineNo">196</span> if (name != null && name.length() > 0) {<a name="line.196"></a> |
| <span class="sourceLineNo">197</span> out.append("Lazy dataset '");<a name="line.197"></a> |
| <span class="sourceLineNo">198</span> out.append(name);<a name="line.198"></a> |
| <span class="sourceLineNo">199</span> out.append("' has shape [");<a name="line.199"></a> |
| <span class="sourceLineNo">200</span> } else {<a name="line.200"></a> |
| <span class="sourceLineNo">201</span> out.append("Lazy dataset shape is [");<a name="line.201"></a> |
| <span class="sourceLineNo">202</span> }<a name="line.202"></a> |
| <span class="sourceLineNo">203</span> int rank = shape == null ? 0 : shape.length;<a name="line.203"></a> |
| <span class="sourceLineNo">204</span><a name="line.204"></a> |
| <span class="sourceLineNo">205</span> if (rank > 0 && shape[0] >= 0) {<a name="line.205"></a> |
| <span class="sourceLineNo">206</span> out.append(shape[0]);<a name="line.206"></a> |
| <span class="sourceLineNo">207</span> }<a name="line.207"></a> |
| <span class="sourceLineNo">208</span> for (int i = 1; i < rank; i++) {<a name="line.208"></a> |
| <span class="sourceLineNo">209</span> out.append(", " + shape[i]);<a name="line.209"></a> |
| <span class="sourceLineNo">210</span> }<a name="line.210"></a> |
| <span class="sourceLineNo">211</span> out.append(']');<a name="line.211"></a> |
| <span class="sourceLineNo">212</span><a name="line.212"></a> |
| <span class="sourceLineNo">213</span> return out.toString();<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> @Override<a name="line.216"></a> |
| <span class="sourceLineNo">217</span> public int hashCode() {<a name="line.217"></a> |
| <span class="sourceLineNo">218</span> final int prime = 31;<a name="line.218"></a> |
| <span class="sourceLineNo">219</span> int result = super.hashCode();<a name="line.219"></a> |
| <span class="sourceLineNo">220</span> result = prime * result + Arrays.hashCode(oShape);<a name="line.220"></a> |
| <span class="sourceLineNo">221</span> result = prime * result + (int) (size ^ (size >>> 32));<a name="line.221"></a> |
| <span class="sourceLineNo">222</span> result = prime * result + clazz.hashCode();<a name="line.222"></a> |
| <span class="sourceLineNo">223</span> result = prime * result + isize;<a name="line.223"></a> |
| <span class="sourceLineNo">224</span> result = prime * result + ((loader == null) ? 0 : loader.hashCode());<a name="line.224"></a> |
| <span class="sourceLineNo">225</span> result = prime * result + Arrays.hashCode(begSlice);<a name="line.225"></a> |
| <span class="sourceLineNo">226</span> result = prime * result + Arrays.hashCode(delSlice);<a name="line.226"></a> |
| <span class="sourceLineNo">227</span> result = prime * result + Arrays.hashCode(sShape);<a name="line.227"></a> |
| <span class="sourceLineNo">228</span> result = prime * result + Arrays.hashCode(padding);<a name="line.228"></a> |
| <span class="sourceLineNo">229</span> result = prime * result + Arrays.hashCode(map);<a name="line.229"></a> |
| <span class="sourceLineNo">230</span> return result;<a name="line.230"></a> |
| <span class="sourceLineNo">231</span> }<a name="line.231"></a> |
| <span class="sourceLineNo">232</span><a name="line.232"></a> |
| <span class="sourceLineNo">233</span> @Override<a name="line.233"></a> |
| <span class="sourceLineNo">234</span> public boolean equals(Object obj) {<a name="line.234"></a> |
| <span class="sourceLineNo">235</span> if (this == obj) {<a name="line.235"></a> |
| <span class="sourceLineNo">236</span> return true;<a name="line.236"></a> |
| <span class="sourceLineNo">237</span> }<a name="line.237"></a> |
| <span class="sourceLineNo">238</span> if (!super.equals(obj)) {<a name="line.238"></a> |
| <span class="sourceLineNo">239</span> return false;<a name="line.239"></a> |
| <span class="sourceLineNo">240</span> }<a name="line.240"></a> |
| <span class="sourceLineNo">241</span><a name="line.241"></a> |
| <span class="sourceLineNo">242</span> LazyDataset other = (LazyDataset) obj;<a name="line.242"></a> |
| <span class="sourceLineNo">243</span> if (!Arrays.equals(oShape, other.oShape)) {<a name="line.243"></a> |
| <span class="sourceLineNo">244</span> return false;<a name="line.244"></a> |
| <span class="sourceLineNo">245</span> }<a name="line.245"></a> |
| <span class="sourceLineNo">246</span> if (size != other.size) {<a name="line.246"></a> |
| <span class="sourceLineNo">247</span> return false;<a name="line.247"></a> |
| <span class="sourceLineNo">248</span> }<a name="line.248"></a> |
| <span class="sourceLineNo">249</span> if (!clazz.equals(other.clazz)) {<a name="line.249"></a> |
| <span class="sourceLineNo">250</span> return false;<a name="line.250"></a> |
| <span class="sourceLineNo">251</span> }<a name="line.251"></a> |
| <span class="sourceLineNo">252</span> if (isize != other.isize) {<a name="line.252"></a> |
| <span class="sourceLineNo">253</span> return false;<a name="line.253"></a> |
| <span class="sourceLineNo">254</span> }<a name="line.254"></a> |
| <span class="sourceLineNo">255</span><a name="line.255"></a> |
| <span class="sourceLineNo">256</span> if (loader != other.loader) {<a name="line.256"></a> |
| <span class="sourceLineNo">257</span> return false;<a name="line.257"></a> |
| <span class="sourceLineNo">258</span> }<a name="line.258"></a> |
| <span class="sourceLineNo">259</span><a name="line.259"></a> |
| <span class="sourceLineNo">260</span> if (!Arrays.equals(begSlice, other.begSlice)) {<a name="line.260"></a> |
| <span class="sourceLineNo">261</span> return false;<a name="line.261"></a> |
| <span class="sourceLineNo">262</span> }<a name="line.262"></a> |
| <span class="sourceLineNo">263</span> if (!Arrays.equals(delSlice, other.delSlice)) {<a name="line.263"></a> |
| <span class="sourceLineNo">264</span> return false;<a name="line.264"></a> |
| <span class="sourceLineNo">265</span> }<a name="line.265"></a> |
| <span class="sourceLineNo">266</span> if (!Arrays.equals(sShape, other.sShape)) {<a name="line.266"></a> |
| <span class="sourceLineNo">267</span> return false;<a name="line.267"></a> |
| <span class="sourceLineNo">268</span> }<a name="line.268"></a> |
| <span class="sourceLineNo">269</span> if (!Arrays.equals(padding, other.padding)) {<a name="line.269"></a> |
| <span class="sourceLineNo">270</span> return false;<a name="line.270"></a> |
| <span class="sourceLineNo">271</span> }<a name="line.271"></a> |
| <span class="sourceLineNo">272</span> if (!Arrays.equals(map, other.map)) {<a name="line.272"></a> |
| <span class="sourceLineNo">273</span> return false;<a name="line.273"></a> |
| <span class="sourceLineNo">274</span> }<a name="line.274"></a> |
| <span class="sourceLineNo">275</span><a name="line.275"></a> |
| <span class="sourceLineNo">276</span> return true;<a name="line.276"></a> |
| <span class="sourceLineNo">277</span> }<a name="line.277"></a> |
| <span class="sourceLineNo">278</span><a name="line.278"></a> |
| <span class="sourceLineNo">279</span> @Override<a name="line.279"></a> |
| <span class="sourceLineNo">280</span> public LazyDataset clone() {<a name="line.280"></a> |
| <span class="sourceLineNo">281</span> return new LazyDataset(this);<a name="line.281"></a> |
| <span class="sourceLineNo">282</span> }<a name="line.282"></a> |
| <span class="sourceLineNo">283</span><a name="line.283"></a> |
| <span class="sourceLineNo">284</span> @Override<a name="line.284"></a> |
| <span class="sourceLineNo">285</span> public void setShape(int... shape) {<a name="line.285"></a> |
| <span class="sourceLineNo">286</span> setShapeInternal(shape.clone());<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> @Override<a name="line.289"></a> |
| <span class="sourceLineNo">290</span> public LazyDataset squeezeEnds() {<a name="line.290"></a> |
| <span class="sourceLineNo">291</span> setShapeInternal(ShapeUtils.squeezeShape(shape, true));<a name="line.291"></a> |
| <span class="sourceLineNo">292</span> return this;<a name="line.292"></a> |
| <span class="sourceLineNo">293</span> }<a name="line.293"></a> |
| <span class="sourceLineNo">294</span><a name="line.294"></a> |
| <span class="sourceLineNo">295</span> @Override<a name="line.295"></a> |
| <span class="sourceLineNo">296</span> public Dataset getSlice(int[] start, int[] stop, int[] step) throws DatasetException {<a name="line.296"></a> |
| <span class="sourceLineNo">297</span> return getSlice(null, start, stop, step);<a name="line.297"></a> |
| <span class="sourceLineNo">298</span> }<a name="line.298"></a> |
| <span class="sourceLineNo">299</span><a name="line.299"></a> |
| <span class="sourceLineNo">300</span> @Override<a name="line.300"></a> |
| <span class="sourceLineNo">301</span> public Dataset getSlice(Slice... slice) throws DatasetException {<a name="line.301"></a> |
| <span class="sourceLineNo">302</span> if (slice == null || slice.length == 0) {<a name="line.302"></a> |
| <span class="sourceLineNo">303</span> return getSlice(null, new SliceND(shape));<a name="line.303"></a> |
| <span class="sourceLineNo">304</span> }<a name="line.304"></a> |
| <span class="sourceLineNo">305</span> return getSlice(null, new SliceND(shape, slice));<a name="line.305"></a> |
| <span class="sourceLineNo">306</span> }<a name="line.306"></a> |
| <span class="sourceLineNo">307</span><a name="line.307"></a> |
| <span class="sourceLineNo">308</span> @Override<a name="line.308"></a> |
| <span class="sourceLineNo">309</span> public Dataset getSlice(SliceND slice) throws DatasetException {<a name="line.309"></a> |
| <span class="sourceLineNo">310</span> return getSlice(null, slice);<a name="line.310"></a> |
| <span class="sourceLineNo">311</span> }<a name="line.311"></a> |
| <span class="sourceLineNo">312</span><a name="line.312"></a> |
| <span class="sourceLineNo">313</span> @Override<a name="line.313"></a> |
| <span class="sourceLineNo">314</span> public Dataset getSlice(IMonitor monitor, Slice... slice) throws DatasetException {<a name="line.314"></a> |
| <span class="sourceLineNo">315</span> if (slice == null || slice.length == 0) {<a name="line.315"></a> |
| <span class="sourceLineNo">316</span> return getSlice(monitor, new SliceND(shape));<a name="line.316"></a> |
| <span class="sourceLineNo">317</span> }<a name="line.317"></a> |
| <span class="sourceLineNo">318</span> return getSlice(monitor, new SliceND(shape, slice));<a name="line.318"></a> |
| <span class="sourceLineNo">319</span> }<a name="line.319"></a> |
| <span class="sourceLineNo">320</span><a name="line.320"></a> |
| <span class="sourceLineNo">321</span> @Override<a name="line.321"></a> |
| <span class="sourceLineNo">322</span> public LazyDataset getSliceView(Slice... slice) {<a name="line.322"></a> |
| <span class="sourceLineNo">323</span> if (slice == null || slice.length == 0) {<a name="line.323"></a> |
| <span class="sourceLineNo">324</span> return getSliceView(new SliceND(shape));<a name="line.324"></a> |
| <span class="sourceLineNo">325</span> }<a name="line.325"></a> |
| <span class="sourceLineNo">326</span> return getSliceView(new SliceND(shape, slice));<a name="line.326"></a> |
| <span class="sourceLineNo">327</span> }<a name="line.327"></a> |
| <span class="sourceLineNo">328</span><a name="line.328"></a> |
| <span class="sourceLineNo">329</span> /**<a name="line.329"></a> |
| <span class="sourceLineNo">330</span> * @param nShape<a name="line.330"></a> |
| <span class="sourceLineNo">331</span> */<a name="line.331"></a> |
| <span class="sourceLineNo">332</span> private void setShapeInternal(int... nShape) {<a name="line.332"></a> |
| <span class="sourceLineNo">333</span> // work out transposed (sliced) shape (instead of removing padding from current shape)<a name="line.333"></a> |
| <span class="sourceLineNo">334</span> if (size != 0) {<a name="line.334"></a> |
| <span class="sourceLineNo">335</span> int[] pShape = calcTransposed(map, sShape == null ? oShape : sShape);<a name="line.335"></a> |
| <span class="sourceLineNo">336</span> padding = ShapeUtils.calcShapePadding(pShape, nShape);<a name="line.336"></a> |
| <span class="sourceLineNo">337</span> }<a name="line.337"></a> |
| <span class="sourceLineNo">338</span><a name="line.338"></a> |
| <span class="sourceLineNo">339</span> if (metadata != null) {<a name="line.339"></a> |
| <span class="sourceLineNo">340</span> storeMetadata(metadata, Reshapeable.class);<a name="line.340"></a> |
| <span class="sourceLineNo">341</span> metadata = copyMetadata();<a name="line.341"></a> |
| <span class="sourceLineNo">342</span> reshapeMetadata(shape, nShape);<a name="line.342"></a> |
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| <span class="sourceLineNo">344</span> shape = nShape;<a name="line.344"></a> |
| <span class="sourceLineNo">345</span> }<a name="line.345"></a> |
| <span class="sourceLineNo">346</span><a name="line.346"></a> |
| <span class="sourceLineNo">347</span> @Override<a name="line.347"></a> |
| <span class="sourceLineNo">348</span> public LazyDataset getSliceView(int[] start, int[] stop, int[] step) {<a name="line.348"></a> |
| <span class="sourceLineNo">349</span> return getSliceView(new SliceND(shape, start, stop, step));<a name="line.349"></a> |
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| <span class="sourceLineNo">351</span><a name="line.351"></a> |
| <span class="sourceLineNo">352</span> @Override<a name="line.352"></a> |
| <span class="sourceLineNo">353</span> public LazyDataset getSliceView(SliceND slice) {<a name="line.353"></a> |
| <span class="sourceLineNo">354</span> LazyDataset view = clone();<a name="line.354"></a> |
| <span class="sourceLineNo">355</span> if (slice.isAll()) {<a name="line.355"></a> |
| <span class="sourceLineNo">356</span> return view;<a name="line.356"></a> |
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| <span class="sourceLineNo">358</span><a name="line.358"></a> |
| <span class="sourceLineNo">359</span> SliceND nslice = calcTrueSlice(slice);<a name="line.359"></a> |
| <span class="sourceLineNo">360</span> if (nslice != null) {<a name="line.360"></a> |
| <span class="sourceLineNo">361</span> view.begSlice = nslice.getStart();<a name="line.361"></a> |
| <span class="sourceLineNo">362</span> view.delSlice = nslice.getStep();<a name="line.362"></a> |
| <span class="sourceLineNo">363</span> view.sShape = nslice.getShape();<a name="line.363"></a> |
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| <span class="sourceLineNo">366</span> view.size = ShapeUtils.calcLongSize(view.shape);<a name="line.366"></a> |
| <span class="sourceLineNo">367</span> view.storeMetadata(metadata, Sliceable.class);<a name="line.367"></a> |
| <span class="sourceLineNo">368</span><a name="line.368"></a> |
| <span class="sourceLineNo">369</span> view.sliceMetadata(true, slice);<a name="line.369"></a> |
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| <span class="sourceLineNo">372</span><a name="line.372"></a> |
| <span class="sourceLineNo">373</span> @Override<a name="line.373"></a> |
| <span class="sourceLineNo">374</span> public Dataset getSlice(IMonitor monitor, int[] start, int[] stop, int[] step) throws DatasetException {<a name="line.374"></a> |
| <span class="sourceLineNo">375</span> return getSlice(monitor, new SliceND(shape, start, stop, step));<a name="line.375"></a> |
| <span class="sourceLineNo">376</span> }<a name="line.376"></a> |
| <span class="sourceLineNo">377</span><a name="line.377"></a> |
| <span class="sourceLineNo">378</span> @Override<a name="line.378"></a> |
| <span class="sourceLineNo">379</span> public Dataset getSlice(IMonitor monitor, SliceND slice) throws DatasetException {<a name="line.379"></a> |
| <span class="sourceLineNo">380</span> if (loader != null && !loader.isFileReadable()) {<a name="line.380"></a> |
| <span class="sourceLineNo">381</span> return null;<a name="line.381"></a> |
| <span class="sourceLineNo">382</span> }<a name="line.382"></a> |
| <span class="sourceLineNo">383</span><a name="line.383"></a> |
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| <span class="sourceLineNo">385</span><a name="line.385"></a> |
| <span class="sourceLineNo">386</span> Dataset a;<a name="line.386"></a> |
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| <span class="sourceLineNo">388</span> a = DatasetFactory.zeros(clazz, slice.getShape());<a name="line.388"></a> |
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| <span class="sourceLineNo">393</span> logger.error("Problem getting {}: {}", String.format("slice %s %s %s from %s", Arrays.toString(slice.getStart()), Arrays.toString(slice.getStop()),<a name="line.393"></a> |
| <span class="sourceLineNo">394</span> Arrays.toString(slice.getStep()), loader), e);<a name="line.394"></a> |
| <span class="sourceLineNo">395</span> throw new DatasetException(e);<a name="line.395"></a> |
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| <span class="sourceLineNo">398</span> a.setName(name + AbstractDataset.BLOCK_OPEN + (nslice == null ? slice : nslice) + AbstractDataset.BLOCK_CLOSE);<a name="line.398"></a> |
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| <span class="sourceLineNo">405</span> // metadata axis may be larger than data<a name="line.405"></a> |
| <span class="sourceLineNo">406</span> if (nslice != null && (!nslice.isAll() || nslice.getMaxShape() != nslice.getShape())) {<a name="line.406"></a> |
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| <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> if (nslice != null) {<a name="line.411"></a> |
| <span class="sourceLineNo">412</span> if (map != null) {<a name="line.412"></a> |
| <span class="sourceLineNo">413</span> a = a.getTransposedView(map);<a name="line.413"></a> |
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| <span class="sourceLineNo">415</span> if (padding != null) {<a name="line.415"></a> |
| <span class="sourceLineNo">416</span> a.setShape(slice.getShape());<a name="line.416"></a> |
| <span class="sourceLineNo">417</span> }<a name="line.417"></a> |
| <span class="sourceLineNo">418</span> }<a name="line.418"></a> |
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| <span class="sourceLineNo">420</span><a name="line.420"></a> |
| <span class="sourceLineNo">421</span> return a;<a name="line.421"></a> |
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| <span class="sourceLineNo">424</span> @Override<a name="line.424"></a> |
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| <span class="sourceLineNo">426</span> LazyDataset view = clone();<a name="line.426"></a> |
| <span class="sourceLineNo">427</span><a name="line.427"></a> |
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| <span class="sourceLineNo">430</span> return view;<a name="line.430"></a> |
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| <span class="sourceLineNo">432</span><a name="line.432"></a> |
| <span class="sourceLineNo">433</span> view.shape = calcTransposed(naxes, shape);<a name="line.433"></a> |
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| <span class="sourceLineNo">436</span> int nr = shape.length;<a name="line.436"></a> |
| <span class="sourceLineNo">437</span> int j = 0; // naxes index<a name="line.437"></a> |
| <span class="sourceLineNo">438</span> int[] mShape = calcTransposed(map, sShape == null ? oShape : sShape); // pre-padded shape<a name="line.438"></a> |
| <span class="sourceLineNo">439</span> int m = 0; // shape index<a name="line.439"></a> |
| <span class="sourceLineNo">440</span> int e = -1; // index of unit dimension<a name="line.440"></a> |
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| <span class="sourceLineNo">442</span> for (int a : naxes) {<a name="line.442"></a> |
| <span class="sourceLineNo">443</span> uaxes.add(a);<a name="line.443"></a> |
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| <span class="sourceLineNo">445</span> List<Integer> oList = new ArrayList<>(); // dimensions left out by padding (in order)<a name="line.445"></a> |
| <span class="sourceLineNo">446</span> int np = padding.length;<a name="line.446"></a> |
| <span class="sourceLineNo">447</span> for (int i = 0; i < np; i++) {<a name="line.447"></a> |
| <span class="sourceLineNo">448</span> int p = padding[i];<a name="line.448"></a> |
| <span class="sourceLineNo">449</span> if (p > 0) { // remove added dimensions<a name="line.449"></a> |
| <span class="sourceLineNo">450</span> for (int k = 0; k < p; k++, j++) {<a name="line.450"></a> |
| <span class="sourceLineNo">451</span> uaxes.remove((Integer) j);<a name="line.451"></a> |
| <span class="sourceLineNo">452</span> }<a name="line.452"></a> |
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| <span class="sourceLineNo">454</span> if (mShape[m] == 1) { // bump up last unit dimension index<a name="line.454"></a> |
| <span class="sourceLineNo">455</span> e = m;<a name="line.455"></a> |
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| <span class="sourceLineNo">457</span> j++;<a name="line.457"></a> |
| <span class="sourceLineNo">458</span> m++;<a name="line.458"></a> |
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| <span class="sourceLineNo">460</span> p = -p;<a name="line.460"></a> |
| <span class="sourceLineNo">461</span> for (int k = 0; k < p; k++) {<a name="line.461"></a> |
| <span class="sourceLineNo">462</span> e = find(mShape, 1, e + 1);<a name="line.462"></a> |
| <span class="sourceLineNo">463</span> oList.add(e);<a name="line.463"></a> |
| <span class="sourceLineNo">464</span> }<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> int[] omitted = new int[oList.size()];<a name="line.468"></a> |
| <span class="sourceLineNo">469</span> j = 0;<a name="line.469"></a> |
| <span class="sourceLineNo">470</span> for (Integer o : oList) {<a name="line.470"></a> |
| <span class="sourceLineNo">471</span> omitted[j++] = o;<a name="line.471"></a> |
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| <span class="sourceLineNo">473</span> int[] used = new int[or - omitted.length]; // all dimensions not omitted in pre-padded shape<a name="line.473"></a> |
| <span class="sourceLineNo">474</span> j = 0;<a name="line.474"></a> |
| <span class="sourceLineNo">475</span> for (int i = 0; i < or; i++) {<a name="line.475"></a> |
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| <span class="sourceLineNo">477</span> used[j++] = i;<a name="line.477"></a> |
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| <span class="sourceLineNo">479</span> }<a name="line.479"></a> |
| <span class="sourceLineNo">480</span><a name="line.480"></a> |
| <span class="sourceLineNo">481</span> int[] vaxes = new int[uaxes.size()];<a name="line.481"></a> |
| <span class="sourceLineNo">482</span> j = 0;<a name="line.482"></a> |
| <span class="sourceLineNo">483</span> for (int i = 0; i < nr; i++) { // remap dimension numbering<a name="line.483"></a> |
| <span class="sourceLineNo">484</span> int l = uaxes.indexOf(i);<a name="line.484"></a> |
| <span class="sourceLineNo">485</span> if (l >= 0) {<a name="line.485"></a> |
| <span class="sourceLineNo">486</span> vaxes[l] = used[j++];<a name="line.486"></a> |
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| <span class="sourceLineNo">488</span> }<a name="line.488"></a> |
| <span class="sourceLineNo">489</span> int[] taxes = new int[or];<a name="line.489"></a> |
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| <span class="sourceLineNo">491</span> for (int i = 0; i < or; i++) { // reassemble map<a name="line.491"></a> |
| <span class="sourceLineNo">492</span> if (Arrays.binarySearch(omitted, i) >= 0) {<a name="line.492"></a> |
| <span class="sourceLineNo">493</span> taxes[i] = i;<a name="line.493"></a> |
| <span class="sourceLineNo">494</span> } else {<a name="line.494"></a> |
| <span class="sourceLineNo">495</span> taxes[i] = vaxes[j++];<a name="line.495"></a> |
| <span class="sourceLineNo">496</span> }<a name="line.496"></a> |
| <span class="sourceLineNo">497</span> }<a name="line.497"></a> |
| <span class="sourceLineNo">498</span><a name="line.498"></a> |
| <span class="sourceLineNo">499</span> naxes = taxes;<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> view.map = map == null ? naxes : calcTransposed(naxes, map);<a name="line.502"></a> |
| <span class="sourceLineNo">503</span> if (view.size != 0) {<a name="line.503"></a> |
| <span class="sourceLineNo">504</span> // work out transposed (sliced) shape<a name="line.504"></a> |
| <span class="sourceLineNo">505</span> int[] tShape = calcTransposed(view.map, sShape == null ? oShape : sShape);<a name="line.505"></a> |
| <span class="sourceLineNo">506</span> try {<a name="line.506"></a> |
| <span class="sourceLineNo">507</span> view.padding = ShapeUtils.calcShapePadding(tShape, view.shape);<a name="line.507"></a> |
| <span class="sourceLineNo">508</span> } catch (IllegalArgumentException e) {<a name="line.508"></a> |
| <span class="sourceLineNo">509</span> System.err.println(e.getMessage() + ": " + Arrays.toString(tShape) + " cf " + Arrays.toString(view.shape));<a name="line.509"></a> |
| <span class="sourceLineNo">510</span> }<a name="line.510"></a> |
| <span class="sourceLineNo">511</span> }<a name="line.511"></a> |
| <span class="sourceLineNo">512</span> view.storeMetadata(metadata, Transposable.class);<a name="line.512"></a> |
| <span class="sourceLineNo">513</span> view.transposeMetadata(axes);<a name="line.513"></a> |
| <span class="sourceLineNo">514</span> return view;<a name="line.514"></a> |
| <span class="sourceLineNo">515</span> }<a name="line.515"></a> |
| <span class="sourceLineNo">516</span><a name="line.516"></a> |
| <span class="sourceLineNo">517</span> private static int find(int[] map, int m, int off) {<a name="line.517"></a> |
| <span class="sourceLineNo">518</span> for (int i = off, imax = map.length; i < imax; i++) {<a name="line.518"></a> |
| <span class="sourceLineNo">519</span> if (map[i] == m) {<a name="line.519"></a> |
| <span class="sourceLineNo">520</span> return i;<a name="line.520"></a> |
| <span class="sourceLineNo">521</span> }<a name="line.521"></a> |
| <span class="sourceLineNo">522</span> }<a name="line.522"></a> |
| <span class="sourceLineNo">523</span> return -1;<a name="line.523"></a> |
| <span class="sourceLineNo">524</span> }<a name="line.524"></a> |
| <span class="sourceLineNo">525</span><a name="line.525"></a> |
| <span class="sourceLineNo">526</span> private static int[] calcTransposed(int[] map, int[] values) {<a name="line.526"></a> |
| <span class="sourceLineNo">527</span> if (values == null) {<a name="line.527"></a> |
| <span class="sourceLineNo">528</span> return null;<a name="line.528"></a> |
| <span class="sourceLineNo">529</span> }<a name="line.529"></a> |
| <span class="sourceLineNo">530</span> int r = values.length;<a name="line.530"></a> |
| <span class="sourceLineNo">531</span> if (map == null || r < 2) {<a name="line.531"></a> |
| <span class="sourceLineNo">532</span> return values;<a name="line.532"></a> |
| <span class="sourceLineNo">533</span> }<a name="line.533"></a> |
| <span class="sourceLineNo">534</span> int[] ovalues = new int[r];<a name="line.534"></a> |
| <span class="sourceLineNo">535</span> for (int i = 0; i < r; i++) {<a name="line.535"></a> |
| <span class="sourceLineNo">536</span> ovalues[i] = values[map[i]];<a name="line.536"></a> |
| <span class="sourceLineNo">537</span> }<a name="line.537"></a> |
| <span class="sourceLineNo">538</span> return ovalues;<a name="line.538"></a> |
| <span class="sourceLineNo">539</span> }<a name="line.539"></a> |
| <span class="sourceLineNo">540</span><a name="line.540"></a> |
| <span class="sourceLineNo">541</span> /**<a name="line.541"></a> |
| <span class="sourceLineNo">542</span> * Calculate absolute slice<a name="line.542"></a> |
| <span class="sourceLineNo">543</span> * @param slice<a name="line.543"></a> |
| <span class="sourceLineNo">544</span> * @return true slice or null if zero-sized<a name="line.544"></a> |
| <span class="sourceLineNo">545</span> */<a name="line.545"></a> |
| <span class="sourceLineNo">546</span> protected final SliceND calcTrueSlice(SliceND slice) {<a name="line.546"></a> |
| <span class="sourceLineNo">547</span> /*<a name="line.547"></a> |
| <span class="sourceLineNo">548</span> * Lazy dataset operations: getTransposedView (T), getSliceView (G), setShape/squeezeEnds (S+/S-):<a name="line.548"></a> |
| <span class="sourceLineNo">549</span> * <a name="line.549"></a> |
| <span class="sourceLineNo">550</span> * . T sets shape, base, and map in new view<a name="line.550"></a> |
| <span class="sourceLineNo">551</span> * . G sets shape, size, begSlice and delSlice in new view<a name="line.551"></a> |
| <span class="sourceLineNo">552</span> * . S sets shape, shapePadding in current view<a name="line.552"></a> |
| <span class="sourceLineNo">553</span> * <a name="line.553"></a> |
| <span class="sourceLineNo">554</span> * Then getSlice needs to interpret all info to find true slice, load data, get transposition (view)<a name="line.554"></a> |
| <span class="sourceLineNo">555</span> * and set shape. Therefore:<a name="line.555"></a> |
| <span class="sourceLineNo">556</span> * . S needs to update shapePadding only<a name="line.556"></a> |
| <span class="sourceLineNo">557</span> * . T needs to update shapePadding too<a name="line.557"></a> |
| <span class="sourceLineNo">558</span> * . G needs to work out true slice to update<a name="line.558"></a> |
| <span class="sourceLineNo">559</span> * <a name="line.559"></a> |
| <span class="sourceLineNo">560</span> * slice -> true slice<a name="line.560"></a> |
| <span class="sourceLineNo">561</span> * adjusts for shape (S^-1) then remap dimensions (T^-1)<a name="line.561"></a> |
| <span class="sourceLineNo">562</span> */<a name="line.562"></a> |
| <span class="sourceLineNo">563</span><a name="line.563"></a> |
| <span class="sourceLineNo">564</span> if (slice == null) {<a name="line.564"></a> |
| <span class="sourceLineNo">565</span> slice = new SliceND(shape);<a name="line.565"></a> |
| <span class="sourceLineNo">566</span> }<a name="line.566"></a> |
| <span class="sourceLineNo">567</span><a name="line.567"></a> |
| <span class="sourceLineNo">568</span> if (ShapeUtils.calcLongSize(slice.getShape()) == 0) {<a name="line.568"></a> |
| <span class="sourceLineNo">569</span> return null;<a name="line.569"></a> |
| <span class="sourceLineNo">570</span> }<a name="line.570"></a> |
| <span class="sourceLineNo">571</span><a name="line.571"></a> |
| <span class="sourceLineNo">572</span> int[] nshape;<a name="line.572"></a> |
| <span class="sourceLineNo">573</span> int[] nstart;<a name="line.573"></a> |
| <span class="sourceLineNo">574</span> int[] nstep;<a name="line.574"></a> |
| <span class="sourceLineNo">575</span><a name="line.575"></a> |
| <span class="sourceLineNo">576</span> int r = oShape.length;<a name="line.576"></a> |
| <span class="sourceLineNo">577</span> if (padding == null) {<a name="line.577"></a> |
| <span class="sourceLineNo">578</span> nshape = slice.getShape();<a name="line.578"></a> |
| <span class="sourceLineNo">579</span> nstart = slice.getStart();<a name="line.579"></a> |
| <span class="sourceLineNo">580</span> nstep = slice.getStep();<a name="line.580"></a> |
| <span class="sourceLineNo">581</span> } else {<a name="line.581"></a> |
| <span class="sourceLineNo">582</span> final int[] lshape = slice.getShape();<a name="line.582"></a> |
| <span class="sourceLineNo">583</span> final int[] lstart = slice.getStart();<a name="line.583"></a> |
| <span class="sourceLineNo">584</span> final int[] lstep = slice.getStep();<a name="line.584"></a> |
| <span class="sourceLineNo">585</span><a name="line.585"></a> |
| <span class="sourceLineNo">586</span> nstart = new int[r];<a name="line.586"></a> |
| <span class="sourceLineNo">587</span> nstep = new int[r];<a name="line.587"></a> |
| <span class="sourceLineNo">588</span> nshape = new int[r];<a name="line.588"></a> |
| <span class="sourceLineNo">589</span> int i = 0;<a name="line.589"></a> |
| <span class="sourceLineNo">590</span> int j = 0;<a name="line.590"></a> |
| <span class="sourceLineNo">591</span> for (int p : padding) { // remove padding<a name="line.591"></a> |
| <span class="sourceLineNo">592</span> if (p == 0) {<a name="line.592"></a> |
| <span class="sourceLineNo">593</span> nshape[i] = lshape[j];<a name="line.593"></a> |
| <span class="sourceLineNo">594</span> nstart[i] = lstart[j];<a name="line.594"></a> |
| <span class="sourceLineNo">595</span> nstep[i] = lstep[j];<a name="line.595"></a> |
| <span class="sourceLineNo">596</span> i++;<a name="line.596"></a> |
| <span class="sourceLineNo">597</span> j++;<a name="line.597"></a> |
| <span class="sourceLineNo">598</span> } else if (p < 0) {<a name="line.598"></a> |
| <span class="sourceLineNo">599</span> int imax = i - p;<a name="line.599"></a> |
| <span class="sourceLineNo">600</span> while (i < imax) {<a name="line.600"></a> |
| <span class="sourceLineNo">601</span> nshape[i] = 1;<a name="line.601"></a> |
| <span class="sourceLineNo">602</span> nstep[i] = 1;<a name="line.602"></a> |
| <span class="sourceLineNo">603</span> i++;<a name="line.603"></a> |
| <span class="sourceLineNo">604</span> }<a name="line.604"></a> |
| <span class="sourceLineNo">605</span> } else {<a name="line.605"></a> |
| <span class="sourceLineNo">606</span> j += p;<a name="line.606"></a> |
| <span class="sourceLineNo">607</span> }<a name="line.607"></a> |
| <span class="sourceLineNo">608</span> }<a name="line.608"></a> |
| <span class="sourceLineNo">609</span> }<a name="line.609"></a> |
| <span class="sourceLineNo">610</span><a name="line.610"></a> |
| <span class="sourceLineNo">611</span> if (map != null && r > 1) { // transpose dimensions<a name="line.611"></a> |
| <span class="sourceLineNo">612</span> int[] pshape = new int[r];<a name="line.612"></a> |
| <span class="sourceLineNo">613</span> int[] pstart = new int[r];<a name="line.613"></a> |
| <span class="sourceLineNo">614</span> int[] pstep = new int[r];<a name="line.614"></a> |
| <span class="sourceLineNo">615</span> for (int i = 0; i < r; i++) {<a name="line.615"></a> |
| <span class="sourceLineNo">616</span> int m = map[i];<a name="line.616"></a> |
| <span class="sourceLineNo">617</span> pshape[m] = nshape[i];<a name="line.617"></a> |
| <span class="sourceLineNo">618</span> pstart[m] = nstart[i];<a name="line.618"></a> |
| <span class="sourceLineNo">619</span> pstep[m] = nstep[i];<a name="line.619"></a> |
| <span class="sourceLineNo">620</span> }<a name="line.620"></a> |
| <span class="sourceLineNo">621</span><a name="line.621"></a> |
| <span class="sourceLineNo">622</span> nshape = pshape;<a name="line.622"></a> |
| <span class="sourceLineNo">623</span> nstart = pstart;<a name="line.623"></a> |
| <span class="sourceLineNo">624</span> nstep = pstep;<a name="line.624"></a> |
| <span class="sourceLineNo">625</span> }<a name="line.625"></a> |
| <span class="sourceLineNo">626</span><a name="line.626"></a> |
| <span class="sourceLineNo">627</span> int[] nstop = new int[r];<a name="line.627"></a> |
| <span class="sourceLineNo">628</span> if (begSlice != null) { // find net slice<a name="line.628"></a> |
| <span class="sourceLineNo">629</span> for (int i = 0; i < r; i++) {<a name="line.629"></a> |
| <span class="sourceLineNo">630</span> int b = begSlice[i];<a name="line.630"></a> |
| <span class="sourceLineNo">631</span> int d = delSlice[i];<a name="line.631"></a> |
| <span class="sourceLineNo">632</span> nstart[i] = b + nstart[i] * d;<a name="line.632"></a> |
| <span class="sourceLineNo">633</span> int nd = nstep[i] * d;<a name="line.633"></a> |
| <span class="sourceLineNo">634</span> nstep[i] = nd;<a name="line.634"></a> |
| <span class="sourceLineNo">635</span> nstop[i] = nstart[i] + (nshape[i] - 1) * nd + (nd >= 0 ? 1 : -1);<a name="line.635"></a> |
| <span class="sourceLineNo">636</span> }<a name="line.636"></a> |
| <span class="sourceLineNo">637</span> } else {<a name="line.637"></a> |
| <span class="sourceLineNo">638</span> for (int i = 0; i < r; i++) {<a name="line.638"></a> |
| <span class="sourceLineNo">639</span> int d = nstep[i];<a name="line.639"></a> |
| <span class="sourceLineNo">640</span> nstop[i] = nstart[i] + (nshape[i] - 1) * d + (d >= 0 ? 1 : -1);<a name="line.640"></a> |
| <span class="sourceLineNo">641</span> }<a name="line.641"></a> |
| <span class="sourceLineNo">642</span> }<a name="line.642"></a> |
| <span class="sourceLineNo">643</span><a name="line.643"></a> |
| <span class="sourceLineNo">644</span> return createSlice(nstart, nstop, nstep);<a name="line.644"></a> |
| <span class="sourceLineNo">645</span> }<a name="line.645"></a> |
| <span class="sourceLineNo">646</span><a name="line.646"></a> |
| <span class="sourceLineNo">647</span> protected SliceND createSlice(int[] nstart, int[] nstop, int[] nstep) {<a name="line.647"></a> |
| <span class="sourceLineNo">648</span> return SliceND.createSlice(oShape, null, nstart, nstop, nstep);<a name="line.648"></a> |
| <span class="sourceLineNo">649</span> }<a name="line.649"></a> |
| <span class="sourceLineNo">650</span><a name="line.650"></a> |
| <span class="sourceLineNo">651</span> /**<a name="line.651"></a> |
| <span class="sourceLineNo">652</span> * Transform data so that it can be used in setSlice of saver<a name="line.652"></a> |
| <span class="sourceLineNo">653</span> * @param data<a name="line.653"></a> |
| <span class="sourceLineNo">654</span> * @param tslice true slice <a name="line.654"></a> |
| <span class="sourceLineNo">655</span> * @return data with dimensions adjusted and remapped <a name="line.655"></a> |
| <span class="sourceLineNo">656</span> */<a name="line.656"></a> |
| <span class="sourceLineNo">657</span> final IDataset transformInput(IDataset data, SliceND tslice) {<a name="line.657"></a> |
| <span class="sourceLineNo">658</span> if (padding != null) { // remove padding<a name="line.658"></a> |
| <span class="sourceLineNo">659</span> data = data.getSliceView();<a name="line.659"></a> |
| <span class="sourceLineNo">660</span> int[] nshape = tslice.getShape();<a name="line.660"></a> |
| <span class="sourceLineNo">661</span> data.setShape(nshape);<a name="line.661"></a> |
| <span class="sourceLineNo">662</span> }<a name="line.662"></a> |
| <span class="sourceLineNo">663</span><a name="line.663"></a> |
| <span class="sourceLineNo">664</span> return map == null ? data : data.getTransposedView(map);<a name="line.664"></a> |
| <span class="sourceLineNo">665</span> }<a name="line.665"></a> |
| <span class="sourceLineNo">666</span><a name="line.666"></a> |
| <span class="sourceLineNo">667</span> /**<a name="line.667"></a> |
| <span class="sourceLineNo">668</span> * Store metadata items that has given annotation<a name="line.668"></a> |
| <span class="sourceLineNo">669</span> * @param origMetadata<a name="line.669"></a> |
| <span class="sourceLineNo">670</span> * @param aclazz<a name="line.670"></a> |
| <span class="sourceLineNo">671</span> */<a name="line.671"></a> |
| <span class="sourceLineNo">672</span> private void storeMetadata(Map<Class<? extends MetadataType>, List<MetadataType>> origMetadata, Class<? extends Annotation> aclazz) {<a name="line.672"></a> |
| <span class="sourceLineNo">673</span> List<Class<? extends MetadataType>> mclazzes = findAnnotatedMetadata(aclazz);<a name="line.673"></a> |
| <span class="sourceLineNo">674</span> if (mclazzes.size() == 0) {<a name="line.674"></a> |
| <span class="sourceLineNo">675</span> return;<a name="line.675"></a> |
| <span class="sourceLineNo">676</span> }<a name="line.676"></a> |
| <span class="sourceLineNo">677</span><a name="line.677"></a> |
| <span class="sourceLineNo">678</span> if (oMetadata == null) {<a name="line.678"></a> |
| <span class="sourceLineNo">679</span> oMetadata = new HashMap<Class<? extends MetadataType>, List<MetadataType>>();<a name="line.679"></a> |
| <span class="sourceLineNo">680</span> }<a name="line.680"></a> |
| <span class="sourceLineNo">681</span> for (Class<? extends MetadataType> mc : mclazzes) {<a name="line.681"></a> |
| <span class="sourceLineNo">682</span> if (oMetadata.containsKey(mc)) {<a name="line.682"></a> |
| <span class="sourceLineNo">683</span> continue; // do not overwrite original<a name="line.683"></a> |
| <span class="sourceLineNo">684</span> }<a name="line.684"></a> |
| <span class="sourceLineNo">685</span><a name="line.685"></a> |
| <span class="sourceLineNo">686</span> List<MetadataType> l = origMetadata.get(mc);<a name="line.686"></a> |
| <span class="sourceLineNo">687</span> List<MetadataType> nl = new ArrayList<MetadataType>(l.size());<a name="line.687"></a> |
| <span class="sourceLineNo">688</span> for (MetadataType m : l) {<a name="line.688"></a> |
| <span class="sourceLineNo">689</span> nl.add(m.clone());<a name="line.689"></a> |
| <span class="sourceLineNo">690</span> }<a name="line.690"></a> |
| <span class="sourceLineNo">691</span> oMetadata.put(mc, nl);<a name="line.691"></a> |
| <span class="sourceLineNo">692</span> }<a name="line.692"></a> |
| <span class="sourceLineNo">693</span> }<a name="line.693"></a> |
| <span class="sourceLineNo">694</span><a name="line.694"></a> |
| <span class="sourceLineNo">695</span> @SuppressWarnings("unchecked")<a name="line.695"></a> |
| <span class="sourceLineNo">696</span> private List<Class<? extends MetadataType>> findAnnotatedMetadata(Class<? extends Annotation> aclazz) {<a name="line.696"></a> |
| <span class="sourceLineNo">697</span> List<Class<? extends MetadataType>> mclazzes = new ArrayList<Class<? extends MetadataType>>();<a name="line.697"></a> |
| <span class="sourceLineNo">698</span> if (metadata == null) {<a name="line.698"></a> |
| <span class="sourceLineNo">699</span> return mclazzes;<a name="line.699"></a> |
| <span class="sourceLineNo">700</span> }<a name="line.700"></a> |
| <span class="sourceLineNo">701</span><a name="line.701"></a> |
| <span class="sourceLineNo">702</span> for (Class<? extends MetadataType> c : metadata.keySet()) {<a name="line.702"></a> |
| <span class="sourceLineNo">703</span> boolean hasAnn = false;<a name="line.703"></a> |
| <span class="sourceLineNo">704</span> for (MetadataType m : metadata.get(c)) {<a name="line.704"></a> |
| <span class="sourceLineNo">705</span> if (m == null) {<a name="line.705"></a> |
| <span class="sourceLineNo">706</span> continue;<a name="line.706"></a> |
| <span class="sourceLineNo">707</span> }<a name="line.707"></a> |
| <span class="sourceLineNo">708</span><a name="line.708"></a> |
| <span class="sourceLineNo">709</span> Class<? extends MetadataType> mc = m.getClass();<a name="line.709"></a> |
| <span class="sourceLineNo">710</span> do { // iterate over super-classes<a name="line.710"></a> |
| <span class="sourceLineNo">711</span> for (Field f : mc.getDeclaredFields()) {<a name="line.711"></a> |
| <span class="sourceLineNo">712</span> if (f.isAnnotationPresent(aclazz)) {<a name="line.712"></a> |
| <span class="sourceLineNo">713</span> hasAnn = true;<a name="line.713"></a> |
| <span class="sourceLineNo">714</span> break;<a name="line.714"></a> |
| <span class="sourceLineNo">715</span> }<a name="line.715"></a> |
| <span class="sourceLineNo">716</span> }<a name="line.716"></a> |
| <span class="sourceLineNo">717</span> Class<?> sclazz = mc.getSuperclass();<a name="line.717"></a> |
| <span class="sourceLineNo">718</span> if (!MetadataType.class.isAssignableFrom(sclazz)) {<a name="line.718"></a> |
| <span class="sourceLineNo">719</span> break;<a name="line.719"></a> |
| <span class="sourceLineNo">720</span> }<a name="line.720"></a> |
| <span class="sourceLineNo">721</span> mc = (Class<? extends MetadataType>) sclazz;<a name="line.721"></a> |
| <span class="sourceLineNo">722</span> } while (!hasAnn);<a name="line.722"></a> |
| <span class="sourceLineNo">723</span> if (hasAnn) {<a name="line.723"></a> |
| <span class="sourceLineNo">724</span> break;<a name="line.724"></a> |
| <span class="sourceLineNo">725</span> }<a name="line.725"></a> |
| <span class="sourceLineNo">726</span> }<a name="line.726"></a> |
| <span class="sourceLineNo">727</span> if (hasAnn) {<a name="line.727"></a> |
| <span class="sourceLineNo">728</span> mclazzes.add(c);<a name="line.728"></a> |
| <span class="sourceLineNo">729</span> }<a name="line.729"></a> |
| <span class="sourceLineNo">730</span> }<a name="line.730"></a> |
| <span class="sourceLineNo">731</span> return mclazzes;<a name="line.731"></a> |
| <span class="sourceLineNo">732</span> }<a name="line.732"></a> |
| <span class="sourceLineNo">733</span><a name="line.733"></a> |
| <span class="sourceLineNo">734</span> /**<a name="line.734"></a> |
| <span class="sourceLineNo">735</span> * Gets the maximum size of a slice of a dataset in a given dimension<a name="line.735"></a> |
| <span class="sourceLineNo">736</span> * which should normally fit in memory. Note that it might be possible<a name="line.736"></a> |
| <span class="sourceLineNo">737</span> * to get more in memory, this is a conservative estimate and seems to<a name="line.737"></a> |
| <span class="sourceLineNo">738</span> * almost always work at the size returned; providing Xmx is less than<a name="line.738"></a> |
| <span class="sourceLineNo">739</span> * the physical memory.<a name="line.739"></a> |
| <span class="sourceLineNo">740</span> * <a name="line.740"></a> |
| <span class="sourceLineNo">741</span> * To get more in memory increase -Xmx setting or use an expression<a name="line.741"></a> |
| <span class="sourceLineNo">742</span> * which calls a rolling function (like rmean) instead of slicing directly<a name="line.742"></a> |
| <span class="sourceLineNo">743</span> * to memory.<a name="line.743"></a> |
| <span class="sourceLineNo">744</span> * <a name="line.744"></a> |
| <span class="sourceLineNo">745</span> * @param lazySet<a name="line.745"></a> |
| <span class="sourceLineNo">746</span> * @param dimension<a name="line.746"></a> |
| <span class="sourceLineNo">747</span> * @return maximum size of dimension that can be sliced.<a name="line.747"></a> |
| <span class="sourceLineNo">748</span> */<a name="line.748"></a> |
| <span class="sourceLineNo">749</span> public static int getMaxSliceLength(ILazyDataset lazySet, int dimension) {<a name="line.749"></a> |
| <span class="sourceLineNo">750</span> // size in bytes of each item<a name="line.750"></a> |
| <span class="sourceLineNo">751</span> final double size = DTypeUtils.getItemBytes(DTypeUtils.getDTypeFromClass(lazySet.getElementClass()), lazySet.getElementsPerItem());<a name="line.751"></a> |
| <span class="sourceLineNo">752</span> <a name="line.752"></a> |
| <span class="sourceLineNo">753</span> // Max in bytes takes into account our minimum requirement<a name="line.753"></a> |
| <span class="sourceLineNo">754</span> final double max = Math.max(Runtime.getRuntime().totalMemory(), Runtime.getRuntime().maxMemory());<a name="line.754"></a> |
| <span class="sourceLineNo">755</span> <a name="line.755"></a> |
| <span class="sourceLineNo">756</span> // Firstly if the whole dataset it likely to fit in memory, then we allow it.<a name="line.756"></a> |
| <span class="sourceLineNo">757</span> // Space specified in bytes per item available<a name="line.757"></a> |
| <span class="sourceLineNo">758</span> final double space = max/lazySet.getSize();<a name="line.758"></a> |
| <span class="sourceLineNo">759</span><a name="line.759"></a> |
| <span class="sourceLineNo">760</span> // If we have room for this whole dataset, then fine<a name="line.760"></a> |
| <span class="sourceLineNo">761</span> int[] shape = lazySet.getShape();<a name="line.761"></a> |
| <span class="sourceLineNo">762</span> if (space >= size) {<a name="line.762"></a> |
| <span class="sourceLineNo">763</span> return shape[dimension];<a name="line.763"></a> |
| <span class="sourceLineNo">764</span> }<a name="line.764"></a> |
| <span class="sourceLineNo">765</span><a name="line.765"></a> |
| <span class="sourceLineNo">766</span> // Otherwise estimate what we can fit in, conservatively.<a name="line.766"></a> |
| <span class="sourceLineNo">767</span> // First get size of one slice, see it that fits, if not, still return 1<a name="line.767"></a> |
| <span class="sourceLineNo">768</span> double sizeOneSlice = size; // in bytes<a name="line.768"></a> |
| <span class="sourceLineNo">769</span> for (int dim = 0; dim < shape.length; dim++) {<a name="line.769"></a> |
| <span class="sourceLineNo">770</span> if (dim == dimension) {<a name="line.770"></a> |
| <span class="sourceLineNo">771</span> continue;<a name="line.771"></a> |
| <span class="sourceLineNo">772</span> }<a name="line.772"></a> |
| <span class="sourceLineNo">773</span> sizeOneSlice *= shape[dim];<a name="line.773"></a> |
| <span class="sourceLineNo">774</span> }<a name="line.774"></a> |
| <span class="sourceLineNo">775</span> double avail = max / sizeOneSlice;<a name="line.775"></a> |
| <span class="sourceLineNo">776</span> if (avail < 1) {<a name="line.776"></a> |
| <span class="sourceLineNo">777</span> return 1;<a name="line.777"></a> |
| <span class="sourceLineNo">778</span> }<a name="line.778"></a> |
| <span class="sourceLineNo">779</span><a name="line.779"></a> |
| <span class="sourceLineNo">780</span> // We fudge this to leave some room<a name="line.780"></a> |
| <span class="sourceLineNo">781</span> return (int) Math.floor(avail/4d);<a name="line.781"></a> |
| <span class="sourceLineNo">782</span> }<a name="line.782"></a> |
| <span class="sourceLineNo">783</span>}<a name="line.783"></a> |
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| </pre> |
| </div> |
| </body> |
| </html> |
