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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.List;<a name="line.22"></a> |
| <span class="sourceLineNo">023</span>import java.util.Map;<a name="line.23"></a> |
| <span class="sourceLineNo">024</span><a name="line.24"></a> |
| <span class="sourceLineNo">025</span>import org.eclipse.january.DatasetException;<a name="line.25"></a> |
| <span class="sourceLineNo">026</span>import org.eclipse.january.IMonitor;<a name="line.26"></a> |
| <span class="sourceLineNo">027</span>import org.eclipse.january.io.ILazyLoader;<a name="line.27"></a> |
| <span class="sourceLineNo">028</span>import org.eclipse.january.metadata.MetadataFactory;<a name="line.28"></a> |
| <span class="sourceLineNo">029</span>import org.eclipse.january.metadata.MetadataType;<a name="line.29"></a> |
| <span class="sourceLineNo">030</span>import org.eclipse.january.metadata.OriginMetadata;<a name="line.30"></a> |
| <span class="sourceLineNo">031</span>import org.eclipse.january.metadata.Reshapeable;<a name="line.31"></a> |
| <span class="sourceLineNo">032</span>import org.eclipse.january.metadata.Sliceable;<a name="line.32"></a> |
| <span class="sourceLineNo">033</span>import org.eclipse.january.metadata.Transposable;<a name="line.33"></a> |
| <span class="sourceLineNo">034</span><a name="line.34"></a> |
| <span class="sourceLineNo">035</span>public class LazyDataset extends LazyDatasetBase implements Serializable, Cloneable {<a name="line.35"></a> |
| <span class="sourceLineNo">036</span> private static final long serialVersionUID = 2467865859867440242L;<a name="line.36"></a> |
| <span class="sourceLineNo">037</span><a name="line.37"></a> |
| <span class="sourceLineNo">038</span> protected int[] oShape; // original shape<a name="line.38"></a> |
| <span class="sourceLineNo">039</span> protected long size; // number of items<a name="line.39"></a> |
| <span class="sourceLineNo">040</span> protected int dtype; // dataset type<a name="line.40"></a> |
| <span class="sourceLineNo">041</span> protected int isize; // number of elements per item<a name="line.41"></a> |
| <span class="sourceLineNo">042</span><a name="line.42"></a> |
| <span class="sourceLineNo">043</span> protected ILazyLoader loader;<a name="line.43"></a> |
| <span class="sourceLineNo">044</span> protected LazyDataset base = null; // used for transpose<a name="line.44"></a> |
| <span class="sourceLineNo">045</span><a name="line.45"></a> |
| <span class="sourceLineNo">046</span> // relative to loader or base<a name="line.46"></a> |
| <span class="sourceLineNo">047</span> protected int prepShape = 0; // prepending and post-pending <a name="line.47"></a> |
| <span class="sourceLineNo">048</span> protected int postShape = 0; // changes to shape<a name="line.48"></a> |
| <span class="sourceLineNo">049</span> protected int[] begSlice = null; // slice begin<a name="line.49"></a> |
| <span class="sourceLineNo">050</span> protected int[] delSlice = null; // slice delta<a name="line.50"></a> |
| <span class="sourceLineNo">051</span> protected int[] map; // transposition map (same length as current shape)<a name="line.51"></a> |
| <span class="sourceLineNo">052</span> protected Map<Class<? extends MetadataType>, List<MetadataType>> oMetadata = null;<a name="line.52"></a> |
| <span class="sourceLineNo">053</span><a name="line.53"></a> |
| <span class="sourceLineNo">054</span> /**<a name="line.54"></a> |
| <span class="sourceLineNo">055</span> * Create a lazy dataset<a name="line.55"></a> |
| <span class="sourceLineNo">056</span> * @param name<a name="line.56"></a> |
| <span class="sourceLineNo">057</span> * @param dtype dataset type<a name="line.57"></a> |
| <span class="sourceLineNo">058</span> * @param elements<a name="line.58"></a> |
| <span class="sourceLineNo">059</span> * @param shape<a name="line.59"></a> |
| <span class="sourceLineNo">060</span> * @param loader<a name="line.60"></a> |
| <span class="sourceLineNo">061</span> */<a name="line.61"></a> |
| <span class="sourceLineNo">062</span> public LazyDataset(String name, int dtype, int elements, int[] shape, ILazyLoader loader) {<a name="line.62"></a> |
| <span class="sourceLineNo">063</span> this.name = name;<a name="line.63"></a> |
| <span class="sourceLineNo">064</span> this.shape = shape.clone();<a name="line.64"></a> |
| <span class="sourceLineNo">065</span> this.oShape = this.shape;<a name="line.65"></a> |
| <span class="sourceLineNo">066</span> this.loader = loader;<a name="line.66"></a> |
| <span class="sourceLineNo">067</span> this.dtype = dtype;<a name="line.67"></a> |
| <span class="sourceLineNo">068</span> this.isize = elements;<a name="line.68"></a> |
| <span class="sourceLineNo">069</span> try {<a name="line.69"></a> |
| <span class="sourceLineNo">070</span> size = ShapeUtils.calcLongSize(shape);<a name="line.70"></a> |
| <span class="sourceLineNo">071</span> } catch (IllegalArgumentException e) {<a name="line.71"></a> |
| <span class="sourceLineNo">072</span> size = Long.MAX_VALUE; // this indicates that the entire dataset cannot be read in! <a name="line.72"></a> |
| <span class="sourceLineNo">073</span> }<a name="line.73"></a> |
| <span class="sourceLineNo">074</span> }<a name="line.74"></a> |
| <span class="sourceLineNo">075</span><a name="line.75"></a> |
| <span class="sourceLineNo">076</span> /**<a name="line.76"></a> |
| <span class="sourceLineNo">077</span> * Create a lazy dataset<a name="line.77"></a> |
| <span class="sourceLineNo">078</span> * @param name<a name="line.78"></a> |
| <span class="sourceLineNo">079</span> * @param dtype dataset type<a name="line.79"></a> |
| <span class="sourceLineNo">080</span> * @param shape<a name="line.80"></a> |
| <span class="sourceLineNo">081</span> * @param loader<a name="line.81"></a> |
| <span class="sourceLineNo">082</span> */<a name="line.82"></a> |
| <span class="sourceLineNo">083</span> public LazyDataset(String name, int dtype, int[] shape, ILazyLoader loader) {<a name="line.83"></a> |
| <span class="sourceLineNo">084</span> this(name, dtype, 1, shape, loader);<a name="line.84"></a> |
| <span class="sourceLineNo">085</span> }<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> * Create a lazy dataset based on in-memory data (handy for testing)<a name="line.88"></a> |
| <span class="sourceLineNo">089</span> * @param dataset<a name="line.89"></a> |
| <span class="sourceLineNo">090</span> */<a name="line.90"></a> |
| <span class="sourceLineNo">091</span> public static LazyDataset createLazyDataset(final Dataset dataset) {<a name="line.91"></a> |
| <span class="sourceLineNo">092</span> return new LazyDataset(dataset.getName(), dataset.getDType(), dataset.getElementsPerItem(), dataset.getShape(),<a name="line.92"></a> |
| <span class="sourceLineNo">093</span> new ILazyLoader() {<a name="line.93"></a> |
| <span class="sourceLineNo">094</span> private static final long serialVersionUID = -6725268922780517523L;<a name="line.94"></a> |
| <span class="sourceLineNo">095</span><a name="line.95"></a> |
| <span class="sourceLineNo">096</span> final Dataset d = dataset;<a name="line.96"></a> |
| <span class="sourceLineNo">097</span> @Override<a name="line.97"></a> |
| <span class="sourceLineNo">098</span> public boolean isFileReadable() {<a name="line.98"></a> |
| <span class="sourceLineNo">099</span> return true;<a name="line.99"></a> |
| <span class="sourceLineNo">100</span> }<a name="line.100"></a> |
| <span class="sourceLineNo">101</span><a name="line.101"></a> |
| <span class="sourceLineNo">102</span> @Override<a name="line.102"></a> |
| <span class="sourceLineNo">103</span> public Dataset getDataset(IMonitor mon, SliceND slice) throws IOException {<a name="line.103"></a> |
| <span class="sourceLineNo">104</span> return d.getSlice(mon, slice);<a name="line.104"></a> |
| <span class="sourceLineNo">105</span> }<a name="line.105"></a> |
| <span class="sourceLineNo">106</span> });<a name="line.106"></a> |
| <span class="sourceLineNo">107</span> }<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> * Can return -1 for unknown<a name="line.110"></a> |
| <span class="sourceLineNo">111</span> */<a name="line.111"></a> |
| <span class="sourceLineNo">112</span> @Override<a name="line.112"></a> |
| <span class="sourceLineNo">113</span> public int getDType() {<a name="line.113"></a> |
| <span class="sourceLineNo">114</span> return dtype;<a name="line.114"></a> |
| <span class="sourceLineNo">115</span> }<a name="line.115"></a> |
| <span class="sourceLineNo">116</span><a name="line.116"></a> |
| <span class="sourceLineNo">117</span> /**<a name="line.117"></a> |
| <span class="sourceLineNo">118</span> * Can return -1 for unknown<a name="line.118"></a> |
| <span class="sourceLineNo">119</span> */<a name="line.119"></a> |
| <span class="sourceLineNo">120</span> @Override<a name="line.120"></a> |
| <span class="sourceLineNo">121</span> public int getElementsPerItem() {<a name="line.121"></a> |
| <span class="sourceLineNo">122</span> return isize;<a name="line.122"></a> |
| <span class="sourceLineNo">123</span> }<a name="line.123"></a> |
| <span class="sourceLineNo">124</span><a name="line.124"></a> |
| <span class="sourceLineNo">125</span> @Override<a name="line.125"></a> |
| <span class="sourceLineNo">126</span> public int getSize() {<a name="line.126"></a> |
| <span class="sourceLineNo">127</span> return (int) size;<a name="line.127"></a> |
| <span class="sourceLineNo">128</span> }<a name="line.128"></a> |
| <span class="sourceLineNo">129</span><a name="line.129"></a> |
| <span class="sourceLineNo">130</span> @Override<a name="line.130"></a> |
| <span class="sourceLineNo">131</span> public String toString() {<a name="line.131"></a> |
| <span class="sourceLineNo">132</span> StringBuilder out = new StringBuilder();<a name="line.132"></a> |
| <span class="sourceLineNo">133</span><a name="line.133"></a> |
| <span class="sourceLineNo">134</span> if (name != null && name.length() > 0) {<a name="line.134"></a> |
| <span class="sourceLineNo">135</span> out.append("Lazy dataset '");<a name="line.135"></a> |
| <span class="sourceLineNo">136</span> out.append(name);<a name="line.136"></a> |
| <span class="sourceLineNo">137</span> out.append("' has shape [");<a name="line.137"></a> |
| <span class="sourceLineNo">138</span> } else {<a name="line.138"></a> |
| <span class="sourceLineNo">139</span> out.append("Lazy dataset shape is [");<a name="line.139"></a> |
| <span class="sourceLineNo">140</span> }<a name="line.140"></a> |
| <span class="sourceLineNo">141</span> int rank = shape == null ? 0 : shape.length;<a name="line.141"></a> |
| <span class="sourceLineNo">142</span><a name="line.142"></a> |
| <span class="sourceLineNo">143</span> if (rank > 0 && shape[0] >= 0) {<a name="line.143"></a> |
| <span class="sourceLineNo">144</span> out.append(shape[0]);<a name="line.144"></a> |
| <span class="sourceLineNo">145</span> }<a name="line.145"></a> |
| <span class="sourceLineNo">146</span> for (int i = 1; i < rank; i++) {<a name="line.146"></a> |
| <span class="sourceLineNo">147</span> out.append(", " + shape[i]);<a name="line.147"></a> |
| <span class="sourceLineNo">148</span> }<a name="line.148"></a> |
| <span class="sourceLineNo">149</span> out.append(']');<a name="line.149"></a> |
| <span class="sourceLineNo">150</span><a name="line.150"></a> |
| <span class="sourceLineNo">151</span> return out.toString();<a name="line.151"></a> |
| <span class="sourceLineNo">152</span> }<a name="line.152"></a> |
| <span class="sourceLineNo">153</span><a name="line.153"></a> |
| <span class="sourceLineNo">154</span> @Override<a name="line.154"></a> |
| <span class="sourceLineNo">155</span> public boolean equals(Object obj) {<a name="line.155"></a> |
| <span class="sourceLineNo">156</span> if (!super.equals(obj))<a name="line.156"></a> |
| <span class="sourceLineNo">157</span> return false;<a name="line.157"></a> |
| <span class="sourceLineNo">158</span><a name="line.158"></a> |
| <span class="sourceLineNo">159</span> LazyDataset other = (LazyDataset) obj;<a name="line.159"></a> |
| <span class="sourceLineNo">160</span> if (dtype != other.dtype) {<a name="line.160"></a> |
| <span class="sourceLineNo">161</span> return false;<a name="line.161"></a> |
| <span class="sourceLineNo">162</span> }<a name="line.162"></a> |
| <span class="sourceLineNo">163</span> if (isize != other.isize) {<a name="line.163"></a> |
| <span class="sourceLineNo">164</span> return false;<a name="line.164"></a> |
| <span class="sourceLineNo">165</span> }<a name="line.165"></a> |
| <span class="sourceLineNo">166</span><a name="line.166"></a> |
| <span class="sourceLineNo">167</span> if (!Arrays.equals(shape, other.shape)) {<a name="line.167"></a> |
| <span class="sourceLineNo">168</span> return false;<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> if (loader != other.loader) {<a name="line.171"></a> |
| <span class="sourceLineNo">172</span> return false;<a name="line.172"></a> |
| <span class="sourceLineNo">173</span> }<a name="line.173"></a> |
| <span class="sourceLineNo">174</span><a name="line.174"></a> |
| <span class="sourceLineNo">175</span> if (prepShape != other.prepShape) {<a name="line.175"></a> |
| <span class="sourceLineNo">176</span> return false;<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> if (postShape != other.postShape) {<a name="line.179"></a> |
| <span class="sourceLineNo">180</span> return false;<a name="line.180"></a> |
| <span class="sourceLineNo">181</span> }<a name="line.181"></a> |
| <span class="sourceLineNo">182</span><a name="line.182"></a> |
| <span class="sourceLineNo">183</span> if (!Arrays.equals(begSlice, other.begSlice)) {<a name="line.183"></a> |
| <span class="sourceLineNo">184</span> return false;<a name="line.184"></a> |
| <span class="sourceLineNo">185</span> }<a name="line.185"></a> |
| <span class="sourceLineNo">186</span> if (!Arrays.equals(delSlice, other.delSlice)) {<a name="line.186"></a> |
| <span class="sourceLineNo">187</span> return false;<a name="line.187"></a> |
| <span class="sourceLineNo">188</span> }<a name="line.188"></a> |
| <span class="sourceLineNo">189</span> if (!Arrays.equals(map, other.map)) {<a name="line.189"></a> |
| <span class="sourceLineNo">190</span> return false;<a name="line.190"></a> |
| <span class="sourceLineNo">191</span> }<a name="line.191"></a> |
| <span class="sourceLineNo">192</span> return true;<a name="line.192"></a> |
| <span class="sourceLineNo">193</span> }<a name="line.193"></a> |
| <span class="sourceLineNo">194</span><a name="line.194"></a> |
| <span class="sourceLineNo">195</span> @Override<a name="line.195"></a> |
| <span class="sourceLineNo">196</span> public LazyDataset clone() {<a name="line.196"></a> |
| <span class="sourceLineNo">197</span> LazyDataset ret = new LazyDataset(new String(name), dtype, isize, oShape, loader);<a name="line.197"></a> |
| <span class="sourceLineNo">198</span> ret.shape = shape;<a name="line.198"></a> |
| <span class="sourceLineNo">199</span> ret.size = size;<a name="line.199"></a> |
| <span class="sourceLineNo">200</span> ret.prepShape = prepShape;<a name="line.200"></a> |
| <span class="sourceLineNo">201</span> ret.postShape = postShape;<a name="line.201"></a> |
| <span class="sourceLineNo">202</span> ret.begSlice = begSlice;<a name="line.202"></a> |
| <span class="sourceLineNo">203</span> ret.delSlice = delSlice;<a name="line.203"></a> |
| <span class="sourceLineNo">204</span> ret.map = map;<a name="line.204"></a> |
| <span class="sourceLineNo">205</span> ret.base = base;<a name="line.205"></a> |
| <span class="sourceLineNo">206</span> ret.metadata = copyMetadata();<a name="line.206"></a> |
| <span class="sourceLineNo">207</span> ret.oMetadata = oMetadata;<a name="line.207"></a> |
| <span class="sourceLineNo">208</span> return ret;<a name="line.208"></a> |
| <span class="sourceLineNo">209</span> }<a name="line.209"></a> |
| <span class="sourceLineNo">210</span><a name="line.210"></a> |
| <span class="sourceLineNo">211</span> @Override<a name="line.211"></a> |
| <span class="sourceLineNo">212</span> public void setShape(int... shape) {<a name="line.212"></a> |
| <span class="sourceLineNo">213</span> setShapeInternal(shape);<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 LazyDataset squeezeEnds() {<a name="line.217"></a> |
| <span class="sourceLineNo">218</span> setShapeInternal(ShapeUtils.squeezeShape(shape, true));<a name="line.218"></a> |
| <span class="sourceLineNo">219</span> return this;<a name="line.219"></a> |
| <span class="sourceLineNo">220</span> }<a name="line.220"></a> |
| <span class="sourceLineNo">221</span><a name="line.221"></a> |
| <span class="sourceLineNo">222</span> @Override<a name="line.222"></a> |
| <span class="sourceLineNo">223</span> public Dataset getSlice(int[] start, int[] stop, int[] step) throws DatasetException {<a name="line.223"></a> |
| <span class="sourceLineNo">224</span> return getSlice(null, start, stop, step);<a name="line.224"></a> |
| <span class="sourceLineNo">225</span> }<a name="line.225"></a> |
| <span class="sourceLineNo">226</span><a name="line.226"></a> |
| <span class="sourceLineNo">227</span> @Override<a name="line.227"></a> |
| <span class="sourceLineNo">228</span> public Dataset getSlice(Slice... slice) throws DatasetException {<a name="line.228"></a> |
| <span class="sourceLineNo">229</span> if (slice == null || slice.length == 0) {<a name="line.229"></a> |
| <span class="sourceLineNo">230</span> return getSlice(null, new SliceND(shape));<a name="line.230"></a> |
| <span class="sourceLineNo">231</span> }<a name="line.231"></a> |
| <span class="sourceLineNo">232</span> return getSlice(null, new SliceND(shape, slice));<a name="line.232"></a> |
| <span class="sourceLineNo">233</span> }<a name="line.233"></a> |
| <span class="sourceLineNo">234</span><a name="line.234"></a> |
| <span class="sourceLineNo">235</span> @Override<a name="line.235"></a> |
| <span class="sourceLineNo">236</span> public Dataset getSlice(SliceND slice) throws DatasetException {<a name="line.236"></a> |
| <span class="sourceLineNo">237</span> return getSlice(null, slice);<a name="line.237"></a> |
| <span class="sourceLineNo">238</span> }<a name="line.238"></a> |
| <span class="sourceLineNo">239</span><a name="line.239"></a> |
| <span class="sourceLineNo">240</span> @Override<a name="line.240"></a> |
| <span class="sourceLineNo">241</span> public Dataset getSlice(IMonitor monitor, Slice... slice) throws DatasetException {<a name="line.241"></a> |
| <span class="sourceLineNo">242</span> if (slice == null || slice.length == 0) {<a name="line.242"></a> |
| <span class="sourceLineNo">243</span> return getSlice(monitor, new SliceND(shape));<a name="line.243"></a> |
| <span class="sourceLineNo">244</span> }<a name="line.244"></a> |
| <span class="sourceLineNo">245</span> return getSlice(monitor, new SliceND(shape, slice));<a name="line.245"></a> |
| <span class="sourceLineNo">246</span> }<a name="line.246"></a> |
| <span class="sourceLineNo">247</span><a name="line.247"></a> |
| <span class="sourceLineNo">248</span> @Override<a name="line.248"></a> |
| <span class="sourceLineNo">249</span> public LazyDataset getSliceView(Slice... slice) {<a name="line.249"></a> |
| <span class="sourceLineNo">250</span> if (slice == null || slice.length == 0) {<a name="line.250"></a> |
| <span class="sourceLineNo">251</span> return getSliceView(new SliceND(shape));<a name="line.251"></a> |
| <span class="sourceLineNo">252</span> }<a name="line.252"></a> |
| <span class="sourceLineNo">253</span> return getSliceView(new SliceND(shape, slice));<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> /**<a name="line.256"></a> |
| <span class="sourceLineNo">257</span> * @param nShape<a name="line.257"></a> |
| <span class="sourceLineNo">258</span> */<a name="line.258"></a> |
| <span class="sourceLineNo">259</span> private void setShapeInternal(int... nShape) {<a name="line.259"></a> |
| <span class="sourceLineNo">260</span> <a name="line.260"></a> |
| <span class="sourceLineNo">261</span> long nsize = ShapeUtils.calcLongSize(nShape);<a name="line.261"></a> |
| <span class="sourceLineNo">262</span> if (nsize != size) {<a name="line.262"></a> |
| <span class="sourceLineNo">263</span> throw new IllegalArgumentException("Size of new shape is not equal to current size");<a name="line.263"></a> |
| <span class="sourceLineNo">264</span> }<a name="line.264"></a> |
| <span class="sourceLineNo">265</span><a name="line.265"></a> |
| <span class="sourceLineNo">266</span> if (nsize == 1) {<a name="line.266"></a> |
| <span class="sourceLineNo">267</span> shape = nShape.clone();<a name="line.267"></a> |
| <span class="sourceLineNo">268</span> return;<a name="line.268"></a> |
| <span class="sourceLineNo">269</span> }<a name="line.269"></a> |
| <span class="sourceLineNo">270</span><a name="line.270"></a> |
| <span class="sourceLineNo">271</span> int ob = -1; // first non-unit dimension<a name="line.271"></a> |
| <span class="sourceLineNo">272</span> int or = shape.length;<a name="line.272"></a> |
| <span class="sourceLineNo">273</span> for (int i = 0; i < or; i++) {<a name="line.273"></a> |
| <span class="sourceLineNo">274</span> if (shape[i] != 1) {<a name="line.274"></a> |
| <span class="sourceLineNo">275</span> ob = i;<a name="line.275"></a> |
| <span class="sourceLineNo">276</span> break;<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> assert ob >= 0;<a name="line.279"></a> |
| <span class="sourceLineNo">280</span> int oe = -1; // last non-unit dimension<a name="line.280"></a> |
| <span class="sourceLineNo">281</span> for (int i = or - 1; i >= ob; i--) {<a name="line.281"></a> |
| <span class="sourceLineNo">282</span> if (shape[i] != 1) {<a name="line.282"></a> |
| <span class="sourceLineNo">283</span> oe = i;<a name="line.283"></a> |
| <span class="sourceLineNo">284</span> break;<a name="line.284"></a> |
| <span class="sourceLineNo">285</span> }<a name="line.285"></a> |
| <span class="sourceLineNo">286</span> }<a name="line.286"></a> |
| <span class="sourceLineNo">287</span> assert oe >= 0;<a name="line.287"></a> |
| <span class="sourceLineNo">288</span> oe++;<a name="line.288"></a> |
| <span class="sourceLineNo">289</span><a name="line.289"></a> |
| <span class="sourceLineNo">290</span> int nb = -1; // first non-unit dimension<a name="line.290"></a> |
| <span class="sourceLineNo">291</span> int nr = nShape.length;<a name="line.291"></a> |
| <span class="sourceLineNo">292</span> for (int i = 0; i < nr; i++) {<a name="line.292"></a> |
| <span class="sourceLineNo">293</span> if (nShape[i] != 1) {<a name="line.293"></a> |
| <span class="sourceLineNo">294</span> nb = i;<a name="line.294"></a> |
| <span class="sourceLineNo">295</span> break;<a name="line.295"></a> |
| <span class="sourceLineNo">296</span> }<a name="line.296"></a> |
| <span class="sourceLineNo">297</span> }<a name="line.297"></a> |
| <span class="sourceLineNo">298</span><a name="line.298"></a> |
| <span class="sourceLineNo">299</span> int i = ob;<a name="line.299"></a> |
| <span class="sourceLineNo">300</span> int j = nb;<a name="line.300"></a> |
| <span class="sourceLineNo">301</span> if (begSlice == null) {<a name="line.301"></a> |
| <span class="sourceLineNo">302</span> for (; i < oe && j < nr; i++, j++) {<a name="line.302"></a> |
| <span class="sourceLineNo">303</span> if (shape[i] != nShape[j]) {<a name="line.303"></a> |
| <span class="sourceLineNo">304</span> throw new IllegalArgumentException("New shape not allowed - can only change shape by adding or removing ones to ends of old shape");<a name="line.304"></a> |
| <span class="sourceLineNo">305</span> }<a name="line.305"></a> |
| <span class="sourceLineNo">306</span> }<a name="line.306"></a> |
| <span class="sourceLineNo">307</span> } else {<a name="line.307"></a> |
| <span class="sourceLineNo">308</span> int[] nBegSlice = new int[nr];<a name="line.308"></a> |
| <span class="sourceLineNo">309</span> int[] nDelSlice = new int[nr];<a name="line.309"></a> |
| <span class="sourceLineNo">310</span> Arrays.fill(nDelSlice, 1);<a name="line.310"></a> |
| <span class="sourceLineNo">311</span> for (; i < oe && j < nr; i++, j++) {<a name="line.311"></a> |
| <span class="sourceLineNo">312</span> if (shape[i] != nShape[j]) {<a name="line.312"></a> |
| <span class="sourceLineNo">313</span> throw new IllegalArgumentException("New shape not allowed - can only change shape by adding or removing ones to ends of old shape");<a name="line.313"></a> |
| <span class="sourceLineNo">314</span> }<a name="line.314"></a> |
| <span class="sourceLineNo">315</span> nBegSlice[j] = begSlice[i];<a name="line.315"></a> |
| <span class="sourceLineNo">316</span> nDelSlice[j] = delSlice[i];<a name="line.316"></a> |
| <span class="sourceLineNo">317</span> }<a name="line.317"></a> |
| <span class="sourceLineNo">318</span> <a name="line.318"></a> |
| <span class="sourceLineNo">319</span> begSlice = nBegSlice;<a name="line.319"></a> |
| <span class="sourceLineNo">320</span> delSlice = nDelSlice;<a name="line.320"></a> |
| <span class="sourceLineNo">321</span> }<a name="line.321"></a> |
| <span class="sourceLineNo">322</span> prepShape += nb - ob;<a name="line.322"></a> |
| <span class="sourceLineNo">323</span> postShape += nr - oe;<a name="line.323"></a> |
| <span class="sourceLineNo">324</span><a name="line.324"></a> |
| <span class="sourceLineNo">325</span> storeMetadata(metadata, Reshapeable.class);<a name="line.325"></a> |
| <span class="sourceLineNo">326</span> metadata = copyMetadata();<a name="line.326"></a> |
| <span class="sourceLineNo">327</span> reshapeMetadata(shape, nShape);<a name="line.327"></a> |
| <span class="sourceLineNo">328</span> shape = nShape;<a name="line.328"></a> |
| <span class="sourceLineNo">329</span> }<a name="line.329"></a> |
| <span class="sourceLineNo">330</span><a name="line.330"></a> |
| <span class="sourceLineNo">331</span> @Override<a name="line.331"></a> |
| <span class="sourceLineNo">332</span> public LazyDataset getSliceView(int[] start, int[] stop, int[] step) {<a name="line.332"></a> |
| <span class="sourceLineNo">333</span> return getSliceView(new SliceND(shape, start, stop, step));<a name="line.333"></a> |
| <span class="sourceLineNo">334</span> }<a name="line.334"></a> |
| <span class="sourceLineNo">335</span><a name="line.335"></a> |
| <span class="sourceLineNo">336</span> @Override<a name="line.336"></a> |
| <span class="sourceLineNo">337</span> public LazyDataset getSliceView(SliceND slice) {<a name="line.337"></a> |
| <span class="sourceLineNo">338</span> LazyDataset view = clone();<a name="line.338"></a> |
| <span class="sourceLineNo">339</span> if (slice.isAll())<a name="line.339"></a> |
| <span class="sourceLineNo">340</span> return view;<a name="line.340"></a> |
| <span class="sourceLineNo">341</span><a name="line.341"></a> |
| <span class="sourceLineNo">342</span> int[] lstart = slice.getStart();<a name="line.342"></a> |
| <span class="sourceLineNo">343</span> int[] lstep = slice.getStep();<a name="line.343"></a> |
| <span class="sourceLineNo">344</span> final int rank = shape.length;<a name="line.344"></a> |
| <span class="sourceLineNo">345</span><a name="line.345"></a> |
| <span class="sourceLineNo">346</span> int[] nShape = slice.getShape();<a name="line.346"></a> |
| <span class="sourceLineNo">347</span> view.shape = nShape;<a name="line.347"></a> |
| <span class="sourceLineNo">348</span> view.size = ShapeUtils.calcLongSize(nShape);<a name="line.348"></a> |
| <span class="sourceLineNo">349</span> if (begSlice == null) {<a name="line.349"></a> |
| <span class="sourceLineNo">350</span> view.begSlice = lstart.clone();<a name="line.350"></a> |
| <span class="sourceLineNo">351</span> view.delSlice = lstep.clone();<a name="line.351"></a> |
| <span class="sourceLineNo">352</span> } else {<a name="line.352"></a> |
| <span class="sourceLineNo">353</span> view.begSlice = new int[rank];<a name="line.353"></a> |
| <span class="sourceLineNo">354</span> view.delSlice = new int[rank];<a name="line.354"></a> |
| <span class="sourceLineNo">355</span> for (int i = 0; i < rank; i++) {<a name="line.355"></a> |
| <span class="sourceLineNo">356</span> view.begSlice[i] = begSlice[i] + lstart[i] * delSlice[i];<a name="line.356"></a> |
| <span class="sourceLineNo">357</span> view.delSlice[i] = delSlice[i] * lstep[i];<a name="line.357"></a> |
| <span class="sourceLineNo">358</span> }<a name="line.358"></a> |
| <span class="sourceLineNo">359</span> }<a name="line.359"></a> |
| <span class="sourceLineNo">360</span> view.storeMetadata(metadata, Sliceable.class);<a name="line.360"></a> |
| <span class="sourceLineNo">361</span> <a name="line.361"></a> |
| <span class="sourceLineNo">362</span> view.sliceMetadata(true, slice);<a name="line.362"></a> |
| <span class="sourceLineNo">363</span> return view;<a name="line.363"></a> |
| <span class="sourceLineNo">364</span> }<a name="line.364"></a> |
| <span class="sourceLineNo">365</span><a name="line.365"></a> |
| <span class="sourceLineNo">366</span> @Override<a name="line.366"></a> |
| <span class="sourceLineNo">367</span> public LazyDataset getTransposedView(int... axes) {<a name="line.367"></a> |
| <span class="sourceLineNo">368</span> LazyDataset view = clone();<a name="line.368"></a> |
| <span class="sourceLineNo">369</span><a name="line.369"></a> |
| <span class="sourceLineNo">370</span> // everything now is seen through a map<a name="line.370"></a> |
| <span class="sourceLineNo">371</span> axes = checkPermutatedAxes(shape, axes);<a name="line.371"></a> |
| <span class="sourceLineNo">372</span> if (axes == null)<a name="line.372"></a> |
| <span class="sourceLineNo">373</span> return view;<a name="line.373"></a> |
| <span class="sourceLineNo">374</span><a name="line.374"></a> |
| <span class="sourceLineNo">375</span> int r = shape.length;<a name="line.375"></a> |
| <span class="sourceLineNo">376</span> view.shape = new int[r];<a name="line.376"></a> |
| <span class="sourceLineNo">377</span> for (int i = 0; i < r; i++) {<a name="line.377"></a> |
| <span class="sourceLineNo">378</span> view.shape[i] = shape[axes[i]];<a name="line.378"></a> |
| <span class="sourceLineNo">379</span> }<a name="line.379"></a> |
| <span class="sourceLineNo">380</span><a name="line.380"></a> |
| <span class="sourceLineNo">381</span> view.prepShape = 0;<a name="line.381"></a> |
| <span class="sourceLineNo">382</span> view.postShape = 0;<a name="line.382"></a> |
| <span class="sourceLineNo">383</span> view.begSlice = null;<a name="line.383"></a> |
| <span class="sourceLineNo">384</span> view.delSlice = null;<a name="line.384"></a> |
| <span class="sourceLineNo">385</span> view.map = axes;<a name="line.385"></a> |
| <span class="sourceLineNo">386</span> view.base = this;<a name="line.386"></a> |
| <span class="sourceLineNo">387</span> view.storeMetadata(metadata, Transposable.class);<a name="line.387"></a> |
| <span class="sourceLineNo">388</span> view.transposeMetadata(axes);<a name="line.388"></a> |
| <span class="sourceLineNo">389</span> return view;<a name="line.389"></a> |
| <span class="sourceLineNo">390</span> }<a name="line.390"></a> |
| <span class="sourceLineNo">391</span><a name="line.391"></a> |
| <span class="sourceLineNo">392</span> @Override<a name="line.392"></a> |
| <span class="sourceLineNo">393</span> public Dataset getSlice(IMonitor monitor, int[] start, int[] stop, int[] step) throws DatasetException {<a name="line.393"></a> |
| <span class="sourceLineNo">394</span> return getSlice(monitor, new SliceND(shape, start, stop, step));<a name="line.394"></a> |
| <span class="sourceLineNo">395</span> }<a name="line.395"></a> |
| <span class="sourceLineNo">396</span><a name="line.396"></a> |
| <span class="sourceLineNo">397</span> @Override<a name="line.397"></a> |
| <span class="sourceLineNo">398</span> public Dataset getSlice(IMonitor monitor, SliceND slice) throws DatasetException {<a name="line.398"></a> |
| <span class="sourceLineNo">399</span><a name="line.399"></a> |
| <span class="sourceLineNo">400</span> if (loader != null && !loader.isFileReadable())<a name="line.400"></a> |
| <span class="sourceLineNo">401</span> return null; // TODO add interaction to use plot (or remote) server to load dataset<a name="line.401"></a> |
| <span class="sourceLineNo">402</span><a name="line.402"></a> |
| <span class="sourceLineNo">403</span> SliceND nslice = calcTrueSlice(slice);<a name="line.403"></a> |
| <span class="sourceLineNo">404</span><a name="line.404"></a> |
| <span class="sourceLineNo">405</span> Dataset a;<a name="line.405"></a> |
| <span class="sourceLineNo">406</span> if (base != null) {<a name="line.406"></a> |
| <span class="sourceLineNo">407</span> a = base.getSlice(monitor, nslice);<a name="line.407"></a> |
| <span class="sourceLineNo">408</span> } else {<a name="line.408"></a> |
| <span class="sourceLineNo">409</span> try {<a name="line.409"></a> |
| <span class="sourceLineNo">410</span> a = DatasetUtils.convertToDataset(loader.getDataset(monitor, nslice));<a name="line.410"></a> |
| <span class="sourceLineNo">411</span> } catch (IOException e) {<a name="line.411"></a> |
| <span class="sourceLineNo">412</span> logger.error("Problem getting {}: {}", String.format("slice %s %s %s from %s", Arrays.toString(slice.getStart()), Arrays.toString(slice.getStop()),<a name="line.412"></a> |
| <span class="sourceLineNo">413</span> Arrays.toString(slice.getStep()), loader), e);<a name="line.413"></a> |
| <span class="sourceLineNo">414</span> throw new DatasetException(e);<a name="line.414"></a> |
| <span class="sourceLineNo">415</span> }<a name="line.415"></a> |
| <span class="sourceLineNo">416</span> a.setName(name + AbstractDataset.BLOCK_OPEN + nslice.toString() + AbstractDataset.BLOCK_CLOSE);<a name="line.416"></a> |
| <span class="sourceLineNo">417</span> if (metadata != null && a instanceof LazyDatasetBase) {<a name="line.417"></a> |
| <span class="sourceLineNo">418</span> LazyDatasetBase ba = (LazyDatasetBase) a;<a name="line.418"></a> |
| <span class="sourceLineNo">419</span> ba.metadata = copyMetadata();<a name="line.419"></a> |
| <span class="sourceLineNo">420</span> if (oMetadata != null)<a name="line.420"></a> |
| <span class="sourceLineNo">421</span> ba.restoreMetadata(oMetadata);<a name="line.421"></a> |
| <span class="sourceLineNo">422</span> //metadata axis may be larger than data<a name="line.422"></a> |
| <span class="sourceLineNo">423</span> if (!nslice.isAll() || nslice.getMaxShape() != nslice.getShape())<a name="line.423"></a> |
| <span class="sourceLineNo">424</span> ba.sliceMetadata(true, nslice);<a name="line.424"></a> |
| <span class="sourceLineNo">425</span> }<a name="line.425"></a> |
| <span class="sourceLineNo">426</span> }<a name="line.426"></a> |
| <span class="sourceLineNo">427</span> if (map != null) {<a name="line.427"></a> |
| <span class="sourceLineNo">428</span> a = a.getTransposedView(map);<a name="line.428"></a> |
| <span class="sourceLineNo">429</span> }<a name="line.429"></a> |
| <span class="sourceLineNo">430</span> if (slice != null)<a name="line.430"></a> |
| <span class="sourceLineNo">431</span> a.setShape(slice.getShape());<a name="line.431"></a> |
| <span class="sourceLineNo">432</span> a.addMetadata(MetadataFactory.createMetadata(OriginMetadata.class, this, nslice.convertToSlice(), oShape, null, name));<a name="line.432"></a> |
| <span class="sourceLineNo">433</span> <a name="line.433"></a> |
| <span class="sourceLineNo">434</span> return a;<a name="line.434"></a> |
| <span class="sourceLineNo">435</span> }<a name="line.435"></a> |
| <span class="sourceLineNo">436</span><a name="line.436"></a> |
| <span class="sourceLineNo">437</span> // reverse transform<a name="line.437"></a> |
| <span class="sourceLineNo">438</span> private int[] getOriginal(int[] values) {<a name="line.438"></a> |
| <span class="sourceLineNo">439</span> if (values == null)<a name="line.439"></a> |
| <span class="sourceLineNo">440</span> return null;<a name="line.440"></a> |
| <span class="sourceLineNo">441</span> int r = values.length;<a name="line.441"></a> |
| <span class="sourceLineNo">442</span> if (map == null || r < 2)<a name="line.442"></a> |
| <span class="sourceLineNo">443</span> return values;<a name="line.443"></a> |
| <span class="sourceLineNo">444</span> int[] ovalues = new int[r];<a name="line.444"></a> |
| <span class="sourceLineNo">445</span> for (int i = 0; i < r; i++) {<a name="line.445"></a> |
| <span class="sourceLineNo">446</span> ovalues[map[i]] = values[i];<a name="line.446"></a> |
| <span class="sourceLineNo">447</span> }<a name="line.447"></a> |
| <span class="sourceLineNo">448</span> return ovalues;<a name="line.448"></a> |
| <span class="sourceLineNo">449</span> }<a name="line.449"></a> |
| <span class="sourceLineNo">450</span><a name="line.450"></a> |
| <span class="sourceLineNo">451</span> protected final SliceND calcTrueSlice(SliceND slice) {<a name="line.451"></a> |
| <span class="sourceLineNo">452</span> if (slice == null) {<a name="line.452"></a> |
| <span class="sourceLineNo">453</span> slice = new SliceND(shape);<a name="line.453"></a> |
| <span class="sourceLineNo">454</span> }<a name="line.454"></a> |
| <span class="sourceLineNo">455</span> int[] lstart = slice.getStart();<a name="line.455"></a> |
| <span class="sourceLineNo">456</span> int[] lstop = slice.getStop();<a name="line.456"></a> |
| <span class="sourceLineNo">457</span> int[] lstep = slice.getStep();<a name="line.457"></a> |
| <span class="sourceLineNo">458</span><a name="line.458"></a> |
| <span class="sourceLineNo">459</span> int[] nstart;<a name="line.459"></a> |
| <span class="sourceLineNo">460</span> int[] nstop;<a name="line.460"></a> |
| <span class="sourceLineNo">461</span> int[] nstep;<a name="line.461"></a> |
| <span class="sourceLineNo">462</span><a name="line.462"></a> |
| <span class="sourceLineNo">463</span> int r = base == null ? oShape.length : base.shape.length;<a name="line.463"></a> |
| <span class="sourceLineNo">464</span> nstart = new int[r];<a name="line.464"></a> |
| <span class="sourceLineNo">465</span> nstop = new int[r];<a name="line.465"></a> |
| <span class="sourceLineNo">466</span> nstep = new int[r];<a name="line.466"></a> |
| <span class="sourceLineNo">467</span> Arrays.fill(nstop, 1);<a name="line.467"></a> |
| <span class="sourceLineNo">468</span> Arrays.fill(nstep, 1);<a name="line.468"></a> |
| <span class="sourceLineNo">469</span> {<a name="line.469"></a> |
| <span class="sourceLineNo">470</span> int i = 0;<a name="line.470"></a> |
| <span class="sourceLineNo">471</span> int j = 0;<a name="line.471"></a> |
| <span class="sourceLineNo">472</span> if (prepShape < 0) { // ignore entries from new slice <a name="line.472"></a> |
| <span class="sourceLineNo">473</span> i = -prepShape;<a name="line.473"></a> |
| <span class="sourceLineNo">474</span> } else if (prepShape > 0) {<a name="line.474"></a> |
| <span class="sourceLineNo">475</span> j = prepShape;<a name="line.475"></a> |
| <span class="sourceLineNo">476</span> }<a name="line.476"></a> |
| <span class="sourceLineNo">477</span> if (begSlice == null) {<a name="line.477"></a> |
| <span class="sourceLineNo">478</span> for (; i < r && j < shape.length; i++, j++) {<a name="line.478"></a> |
| <span class="sourceLineNo">479</span> nstart[i] = lstart[j];<a name="line.479"></a> |
| <span class="sourceLineNo">480</span> nstop[i] = lstop[j];<a name="line.480"></a> |
| <span class="sourceLineNo">481</span> int d = lstep[j];<a name="line.481"></a> |
| <span class="sourceLineNo">482</span> if (d < 0 && nstop[i] < 0) { // need to wrap around further<a name="line.482"></a> |
| <span class="sourceLineNo">483</span> int l = base == null ? oShape[j]: base.shape[j];<a name="line.483"></a> |
| <span class="sourceLineNo">484</span> nstop[i] -= l;<a name="line.484"></a> |
| <span class="sourceLineNo">485</span> }<a name="line.485"></a> |
| <span class="sourceLineNo">486</span> nstep[i] = d;<a name="line.486"></a> |
| <span class="sourceLineNo">487</span> }<a name="line.487"></a> |
| <span class="sourceLineNo">488</span> } else {<a name="line.488"></a> |
| <span class="sourceLineNo">489</span> for (; i < r && j < shape.length; i++, j++) {<a name="line.489"></a> |
| <span class="sourceLineNo">490</span> int b = begSlice[j];<a name="line.490"></a> |
| <span class="sourceLineNo">491</span> int d = delSlice[j];<a name="line.491"></a> |
| <span class="sourceLineNo">492</span> nstart[i] = b + lstart[j] * d;<a name="line.492"></a> |
| <span class="sourceLineNo">493</span> nstop[i] = b + (lstop[j] - 1) * d + (d >= 0 ? 1 : -1);<a name="line.493"></a> |
| <span class="sourceLineNo">494</span> if (d < 0 && nstop[i] < 0) { // need to wrap around further<a name="line.494"></a> |
| <span class="sourceLineNo">495</span> int l = base == null ? oShape[j]: base.shape[j];<a name="line.495"></a> |
| <span class="sourceLineNo">496</span> nstop[i] -= l;<a name="line.496"></a> |
| <span class="sourceLineNo">497</span> }<a name="line.497"></a> |
| <span class="sourceLineNo">498</span> nstep[i] = lstep[j] * d;<a name="line.498"></a> |
| <span class="sourceLineNo">499</span> }<a name="line.499"></a> |
| <span class="sourceLineNo">500</span> }<a name="line.500"></a> |
| <span class="sourceLineNo">501</span> if (map != null) {<a name="line.501"></a> |
| <span class="sourceLineNo">502</span> nstart = getOriginal(nstart);<a name="line.502"></a> |
| <span class="sourceLineNo">503</span> nstop = getOriginal(nstop);<a name="line.503"></a> |
| <span class="sourceLineNo">504</span> nstep = getOriginal(nstep);<a name="line.504"></a> |
| <span class="sourceLineNo">505</span> }<a name="line.505"></a> |
| <span class="sourceLineNo">506</span> }<a name="line.506"></a> |
| <span class="sourceLineNo">507</span><a name="line.507"></a> |
| <span class="sourceLineNo">508</span> return createSlice(nstart, nstop, nstep);<a name="line.508"></a> |
| <span class="sourceLineNo">509</span> }<a name="line.509"></a> |
| <span class="sourceLineNo">510</span><a name="line.510"></a> |
| <span class="sourceLineNo">511</span> protected final IDataset transformInput(IDataset data) {<a name="line.511"></a> |
| <span class="sourceLineNo">512</span> if (map == null)<a name="line.512"></a> |
| <span class="sourceLineNo">513</span> return data;<a name="line.513"></a> |
| <span class="sourceLineNo">514</span> return data.getTransposedView(map);<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> protected SliceND createSlice(int[] nstart, int[] nstop, int[] nstep) {<a name="line.517"></a> |
| <span class="sourceLineNo">518</span> return new SliceND(base == null ? oShape : base.shape, nstart, nstop, nstep);<a name="line.518"></a> |
| <span class="sourceLineNo">519</span> }<a name="line.519"></a> |
| <span class="sourceLineNo">520</span><a name="line.520"></a> |
| <span class="sourceLineNo">521</span> /**<a name="line.521"></a> |
| <span class="sourceLineNo">522</span> * Store metadata items that has given annotation<a name="line.522"></a> |
| <span class="sourceLineNo">523</span> * @param origMetadata<a name="line.523"></a> |
| <span class="sourceLineNo">524</span> * @param aclazz<a name="line.524"></a> |
| <span class="sourceLineNo">525</span> */<a name="line.525"></a> |
| <span class="sourceLineNo">526</span> private void storeMetadata(Map<Class<? extends MetadataType>, List<MetadataType>> origMetadata, Class<? extends Annotation> aclazz) {<a name="line.526"></a> |
| <span class="sourceLineNo">527</span> List<Class<? extends MetadataType>> mclazzes = findAnnotatedMetadata(aclazz);<a name="line.527"></a> |
| <span class="sourceLineNo">528</span> if (mclazzes.size() == 0)<a name="line.528"></a> |
| <span class="sourceLineNo">529</span> return;<a name="line.529"></a> |
| <span class="sourceLineNo">530</span><a name="line.530"></a> |
| <span class="sourceLineNo">531</span> if (oMetadata == null) {<a name="line.531"></a> |
| <span class="sourceLineNo">532</span> oMetadata = new HashMap<Class<? extends MetadataType>, List<MetadataType>>();<a name="line.532"></a> |
| <span class="sourceLineNo">533</span> }<a name="line.533"></a> |
| <span class="sourceLineNo">534</span> for (Class<? extends MetadataType> mc : mclazzes) {<a name="line.534"></a> |
| <span class="sourceLineNo">535</span> if (oMetadata.containsKey(mc))<a name="line.535"></a> |
| <span class="sourceLineNo">536</span> continue; // do not overwrite original<a name="line.536"></a> |
| <span class="sourceLineNo">537</span><a name="line.537"></a> |
| <span class="sourceLineNo">538</span> List<MetadataType> l = origMetadata.get(mc);<a name="line.538"></a> |
| <span class="sourceLineNo">539</span> List<MetadataType> nl = new ArrayList<MetadataType>(l.size());<a name="line.539"></a> |
| <span class="sourceLineNo">540</span> for (MetadataType m : l) {<a name="line.540"></a> |
| <span class="sourceLineNo">541</span> nl.add(m.clone());<a name="line.541"></a> |
| <span class="sourceLineNo">542</span> }<a name="line.542"></a> |
| <span class="sourceLineNo">543</span> oMetadata.put(mc, nl);<a name="line.543"></a> |
| <span class="sourceLineNo">544</span> }<a name="line.544"></a> |
| <span class="sourceLineNo">545</span> }<a name="line.545"></a> |
| <span class="sourceLineNo">546</span><a name="line.546"></a> |
| <span class="sourceLineNo">547</span> @SuppressWarnings("unchecked")<a name="line.547"></a> |
| <span class="sourceLineNo">548</span> private List<Class<? extends MetadataType>> findAnnotatedMetadata(Class<? extends Annotation> aclazz) {<a name="line.548"></a> |
| <span class="sourceLineNo">549</span> List<Class<? extends MetadataType>> mclazzes = new ArrayList<Class<? extends MetadataType>>();<a name="line.549"></a> |
| <span class="sourceLineNo">550</span> if (metadata == null)<a name="line.550"></a> |
| <span class="sourceLineNo">551</span> return mclazzes;<a name="line.551"></a> |
| <span class="sourceLineNo">552</span><a name="line.552"></a> |
| <span class="sourceLineNo">553</span> for (Class<? extends MetadataType> c : metadata.keySet()) {<a name="line.553"></a> |
| <span class="sourceLineNo">554</span> boolean hasAnn = false;<a name="line.554"></a> |
| <span class="sourceLineNo">555</span> for (MetadataType m : metadata.get(c)) {<a name="line.555"></a> |
| <span class="sourceLineNo">556</span> if (m == null)<a name="line.556"></a> |
| <span class="sourceLineNo">557</span> continue;<a name="line.557"></a> |
| <span class="sourceLineNo">558</span><a name="line.558"></a> |
| <span class="sourceLineNo">559</span> Class<? extends MetadataType> mc = m.getClass();<a name="line.559"></a> |
| <span class="sourceLineNo">560</span> do { // iterate over super-classes<a name="line.560"></a> |
| <span class="sourceLineNo">561</span> for (Field f : mc.getDeclaredFields()) {<a name="line.561"></a> |
| <span class="sourceLineNo">562</span> if (f.isAnnotationPresent(aclazz)) {<a name="line.562"></a> |
| <span class="sourceLineNo">563</span> hasAnn = true;<a name="line.563"></a> |
| <span class="sourceLineNo">564</span> break;<a name="line.564"></a> |
| <span class="sourceLineNo">565</span> }<a name="line.565"></a> |
| <span class="sourceLineNo">566</span> }<a name="line.566"></a> |
| <span class="sourceLineNo">567</span> Class<?> sclazz = mc.getSuperclass();<a name="line.567"></a> |
| <span class="sourceLineNo">568</span> if (!MetadataType.class.isAssignableFrom(sclazz))<a name="line.568"></a> |
| <span class="sourceLineNo">569</span> break;<a name="line.569"></a> |
| <span class="sourceLineNo">570</span> mc = (Class<? extends MetadataType>) sclazz;<a name="line.570"></a> |
| <span class="sourceLineNo">571</span> } while (!hasAnn);<a name="line.571"></a> |
| <span class="sourceLineNo">572</span> if (hasAnn)<a name="line.572"></a> |
| <span class="sourceLineNo">573</span> break;<a name="line.573"></a> |
| <span class="sourceLineNo">574</span> }<a name="line.574"></a> |
| <span class="sourceLineNo">575</span> if (hasAnn) {<a name="line.575"></a> |
| <span class="sourceLineNo">576</span> mclazzes.add(c);<a name="line.576"></a> |
| <span class="sourceLineNo">577</span> }<a name="line.577"></a> |
| <span class="sourceLineNo">578</span> }<a name="line.578"></a> |
| <span class="sourceLineNo">579</span> return mclazzes;<a name="line.579"></a> |
| <span class="sourceLineNo">580</span> }<a name="line.580"></a> |
| <span class="sourceLineNo">581</span><a name="line.581"></a> |
| <span class="sourceLineNo">582</span> /**<a name="line.582"></a> |
| <span class="sourceLineNo">583</span> * Gets the maximum size of a slice of a dataset in a given dimension<a name="line.583"></a> |
| <span class="sourceLineNo">584</span> * which should normally fit in memory. Note that it might be possible<a name="line.584"></a> |
| <span class="sourceLineNo">585</span> * to get more in memory, this is a conservative estimate and seems to<a name="line.585"></a> |
| <span class="sourceLineNo">586</span> * almost always work at the size returned; providing Xmx is less than<a name="line.586"></a> |
| <span class="sourceLineNo">587</span> * the physical memory.<a name="line.587"></a> |
| <span class="sourceLineNo">588</span> * <a name="line.588"></a> |
| <span class="sourceLineNo">589</span> * To get more in memory increase -Xmx setting or use an expression<a name="line.589"></a> |
| <span class="sourceLineNo">590</span> * which calls a rolling function (like rmean) instead of slicing directly<a name="line.590"></a> |
| <span class="sourceLineNo">591</span> * to memory.<a name="line.591"></a> |
| <span class="sourceLineNo">592</span> * <a name="line.592"></a> |
| <span class="sourceLineNo">593</span> * @param lazySet<a name="line.593"></a> |
| <span class="sourceLineNo">594</span> * @param dimension<a name="line.594"></a> |
| <span class="sourceLineNo">595</span> * @return maximum size of dimension that can be sliced.<a name="line.595"></a> |
| <span class="sourceLineNo">596</span> */<a name="line.596"></a> |
| <span class="sourceLineNo">597</span> public static int getMaxSliceLength(ILazyDataset lazySet, int dimension) {<a name="line.597"></a> |
| <span class="sourceLineNo">598</span> // size in bytes of each item<a name="line.598"></a> |
| <span class="sourceLineNo">599</span> final double size = DTypeUtils.getItemBytes(DTypeUtils.getDTypeFromClass(lazySet.getElementClass()), lazySet.getElementsPerItem());<a name="line.599"></a> |
| <span class="sourceLineNo">600</span> <a name="line.600"></a> |
| <span class="sourceLineNo">601</span> // Max in bytes takes into account our minimum requirement<a name="line.601"></a> |
| <span class="sourceLineNo">602</span> final double max = Math.max(Runtime.getRuntime().totalMemory(), Runtime.getRuntime().maxMemory());<a name="line.602"></a> |
| <span class="sourceLineNo">603</span> <a name="line.603"></a> |
| <span class="sourceLineNo">604</span> // Firstly if the whole dataset it likely to fit in memory, then we allow it.<a name="line.604"></a> |
| <span class="sourceLineNo">605</span> // Space specified in bytes per item available<a name="line.605"></a> |
| <span class="sourceLineNo">606</span> final double space = max/lazySet.getSize();<a name="line.606"></a> |
| <span class="sourceLineNo">607</span><a name="line.607"></a> |
| <span class="sourceLineNo">608</span> // If we have room for this whole dataset, then fine<a name="line.608"></a> |
| <span class="sourceLineNo">609</span> int[] shape = lazySet.getShape();<a name="line.609"></a> |
| <span class="sourceLineNo">610</span> if (space >= size)<a name="line.610"></a> |
| <span class="sourceLineNo">611</span> return shape[dimension];<a name="line.611"></a> |
| <span class="sourceLineNo">612</span> <a name="line.612"></a> |
| <span class="sourceLineNo">613</span> // Otherwise estimate what we can fit in, conservatively.<a name="line.613"></a> |
| <span class="sourceLineNo">614</span> // First get size of one slice, see it that fits, if not, still return 1<a name="line.614"></a> |
| <span class="sourceLineNo">615</span> double sizeOneSlice = size; // in bytes<a name="line.615"></a> |
| <span class="sourceLineNo">616</span> for (int dim = 0; dim < shape.length; dim++) {<a name="line.616"></a> |
| <span class="sourceLineNo">617</span> if (dim == dimension)<a name="line.617"></a> |
| <span class="sourceLineNo">618</span> continue;<a name="line.618"></a> |
| <span class="sourceLineNo">619</span> sizeOneSlice *= shape[dim];<a name="line.619"></a> |
| <span class="sourceLineNo">620</span> }<a name="line.620"></a> |
| <span class="sourceLineNo">621</span> double avail = max / sizeOneSlice;<a name="line.621"></a> |
| <span class="sourceLineNo">622</span> if (avail < 1)<a name="line.622"></a> |
| <span class="sourceLineNo">623</span> return 1;<a name="line.623"></a> |
| <span class="sourceLineNo">624</span><a name="line.624"></a> |
| <span class="sourceLineNo">625</span> // We fudge this to leave some room<a name="line.625"></a> |
| <span class="sourceLineNo">626</span> return (int) Math.floor(avail/4d);<a name="line.626"></a> |
| <span class="sourceLineNo">627</span> }<a name="line.627"></a> |
| <span class="sourceLineNo">628</span>}<a name="line.628"></a> |
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| </pre> |
| </div> |
| </body> |
| </html> |
