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<p class="MsoNormal">In the process of working with the Flex reader and finding a temporary solution, I have found what may be a bug:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="text-autospace:none"><u><span style="font-size:10.0pt;font-family:Consolas;color:#0066CC">java.lang.IndexOutOfBoundsException</span></u><span style="font-size:10.0pt;font-family:Consolas;color:red">: Index: 1, Size: 1</span><span style="font-size:10.0pt;font-family:Consolas"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:Consolas;color:red"> at java.util.ArrayList.rangeCheck(Unknown Source)</span><span style="font-size:10.0pt;font-family:Consolas"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:Consolas;color:red"> at java.util.ArrayList.get(Unknown Source)</span><span style="font-size:10.0pt;font-family:Consolas"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:Consolas;color:red"> at ome.xml.model.Pixels.getChannel(</span><u><span style="font-size:10.0pt;font-family:Consolas;color:#0066CC">Pixels.java:573</span></u><span style="font-size:10.0pt;font-family:Consolas;color:red">)</span><span style="font-size:10.0pt;font-family:Consolas"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:Consolas;color:red"> at ome.xml.meta.OMEXMLMetadataImpl.getChannelName(</span><u><span style="font-size:10.0pt;font-family:Consolas;color:#0066CC">OMEXMLMetadataImpl.java:1053</span></u><span style="font-size:10.0pt;font-family:Consolas;color:red">)</span><span style="font-size:10.0pt;font-family:Consolas"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas;color:red"> at org.gnf.HCIReaders.HCIReaderOpera.setWellImagesProps(</span><u><span style="font-size:10.0pt;font-family:Consolas;color:#0066CC">HCIReaderOpera.java:161</span></u><span style="font-size:10.0pt;font-family:Consolas;color:red">)</span><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">In the past the <span style="font-size:10.0pt;font-family:Consolas;color:red">ome.xml.model.Pixels.getChannel()</span> returned null if it did not exist. I have figured out that in my case, I need to invert
<span style="font-size:9.0pt;font-family:"Courier New";color:#353833;background:white">
int imageIndex, int channelIndex</span>, which is probably caused by the bug in handling the flex format from v2.0. However, I think that either the out-of bound exception should be handled internally and that the value null should be returned (I think this
was the default behavior), or that the method should throw an error of its own, which a programmer would know to handle externally.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"">Ghislain Bonamy, PhD<o:p></o:p></span></p>
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