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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Thanks Ray,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Aha – that makes sense.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">It looks like there might be something wrong with my nxs file (attached). In my example Python can’t do a type conversion to the numbers,
but in the chopper example it works fine (see below). We seem to have some extra square brackets – I don’t know if that is significant.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Steve<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">## Diamond example<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">n.entry1.default.ic1monitor<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Out[204]: NXlink('['/entry1/instrument/ic1monitor/ic1monitor']')<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">n.entry1.default.ic1monitor+0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Traceback (most recent call last):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> File "<ipython-input-205-336afb990d12>", line 1, in <module><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> n.entry1.default.ic1monitor+0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> File "build/bdist.linux-x86_64/egg/nexusformat/nexus/tree.py", line 2259, in __add__<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> return NXfield(value=self.nxdata+other, name=self.nxname,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">TypeError: unsupported operand type(s) for +: 'NoneType' and 'int<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">## chopper example<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">c.entry.data.polar_angle<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Out[202]: NXlink('/entry/instrument/detector/polar_angle')<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">c.entry.data.polar_angle+0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Out[203]:
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">NXfield(array([ -7.19999981, -6.5999999 , -6. , ..., 116.3999939 ,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> 116.99999237, 117.59999084], dtype=float32))<o:p></o:p></span></p>
<p class="MsoNormal"><a name="_MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></a></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> NeXus [mailto:nexus-bounces@nexusformat.org]
<b>On Behalf Of </b>Osborn, Raymond<br>
<b>Sent:</b> 14 June 2017 14:13<br>
<b>To:</b> Discussion forum for the NeXus data format <nexus@nexusformat.org><br>
<b>Subject:</b> Re: [Nexus] Nexpy<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Steve,<o:p></o:p></p>
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<p class="MsoNormal">The NeXus format has, since its inception, had the concept that there is a parent object for each link, defined by the attribute ‘target’, even though linked data are stored in HDF5 files as hard links. NeXpy, or rather the underlying nexusformat
API, is designed to make that association clear, whereas h5py makes no such distinction. I’m not sure if there is even a way for h5py to tell what groups an object has been added to without checking object ids. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">If you have a recent version of NeXpy installed, you can open the example file, ‘chopper.nxs’, from the Help menu. I will use it to discuss why I believe it handles links appropriately. In ‘chopper.nxs’, the data group contains two links.
Here are edited selections from the file tree:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">entry:NXentry<o:p></o:p></p>
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<p class="MsoNormal"> data:NXdata<o:p></o:p></p>
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<p class="MsoNormal"> polar_angle -> /entry/instrument/detector/polar_angle<o:p></o:p></p>
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<p class="MsoNormal"> instrument:NXinstrument<o:p></o:p></p>
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<p class="MsoNormal"> detector:NXdetector<o:p></o:p></p>
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<p class="MsoNormal"> polar_angle = float32(148)<o:p></o:p></p>
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<p class="MsoNormal"> @target = '/entry/instrument/detector/polar_angle'<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">So ‘/entry/data/polar_angle’ and ‘/entry/instrument/detector/polar_angle’ are both paths to the same HDF5 object, but the parent object is deemed by the NeXus format to be the latter, as specified by its target attribute. NeXpy chooses
to display the other instance, in ‘/entry/data’ as a link to make this clear.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">>>> chopper.entry.data.polar_angle<o:p></o:p></p>
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<p class="MsoNormal">NXlink('/entry/instrument/detector/polar_angle')<o:p></o:p></p>
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<p class="MsoNormal">>>> chopper.entry.instrument.detector.polar_angle<o:p></o:p></p>
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<p class="MsoNormal">NXfield(array([ -7.19999981, -6.5999999 , -6. , ..., 116.3999939 ,<o:p></o:p></p>
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<p class="MsoNormal"> 116.99999237, 117.59999084], dtype=float32))<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">If you want to know what the parent object is, you can use the NXlink’s ‘nxlink’ attribute, which returns the parent.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">>>> chopper.entry.data.polar_angle.nxlink<o:p></o:p></p>
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<div>
<p class="MsoNormal">NXfield(array([ -7.19999981, -6.5999999 , -6. , ..., 116.3999939 ,<o:p></o:p></p>
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<p class="MsoNormal"> 116.99999237, 117.59999084], dtype=float32))<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Within the NeXpy GUI, you can right-click on the link, which has a chain link icon by it, to display the parent. There is no way to do this in a generic HDF5 viewer.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">In practice, the fact that ‘/entry/data/polar_angle’ is an NXlink object should make no difference in your use of the data. For example, you can check its dtype or shape, and use fields in arithmetic expressions on either the parent or
the link.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
</div>
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<div>
<p class="MsoNormal">>>> chopper.entry.data.polar_angle + 100.0<o:p></o:p></p>
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<div>
<p class="MsoNormal">NXfield(array([ 92.80000305, 93.40000153, 94. , ..., 216.3999939 ,<o:p></o:p></p>
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<div>
<p class="MsoNormal"> 217. , 217.59999084], dtype=float32))<o:p></o:p></p>
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<p class="MsoNormal">>>> chopper.entry.instrument.detector.polar_angle + 100.0<o:p></o:p></p>
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<div>
<p class="MsoNormal">NXfield(array([ 92.80000305, 93.40000153, 94. , ..., 216.3999939 ,<o:p></o:p></p>
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<p class="MsoNormal"> 217. , 217.59999084], dtype=float32))<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I think this is the right way to handle links. In h5py, you could update a dataset’s value without knowing that it has the side effect of changing its value in another group. In NeXpy, the existence of the link is clear but it shouldn’t
impede your use of its values or attributes. I would welcome further comments if you think these are not the right calls.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">With best regards,<o:p></o:p></p>
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<p class="MsoNormal">Ray<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
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<p class="MsoNormal">On Jun 14, 2017, at 6:13 AM, <a href="mailto:steve.collins@diamond.ac.uk">
steve.collins@diamond.ac.uk</a> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Hello,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">I’d like to subscribe to this email list. I’m not sure if it is appropriate to ask a technical question here, but here is one anyway (I hope it’s OK):<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">I have a question about the Python Nexusformat/NeXpy nxload method.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">I seem to have problems reading data entries that have been defined using links. That is, the method returns an NXlink object rather than the actual data:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">n.entry1.default.ic1monitor<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Out[143]: NXlink('['/entry1/instrument/ic1monitor/ic1monitor']')<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">If I use h5py directly then I get the dataset:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">h['/entry1/default/ic1monitor']<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Out[144]: <HDF5 dataset "ic1monitor": shape (10001,), type "<f8"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Is this expected or am I doing something wrong? I read in the manual that all data are specified via links so there is no distinction between the 'original' data and a link.
Is that right?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Thank you for your help.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Regards,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Steve Collins (Diamond Light Source)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">P.S. I can send you the data files and Python code of course, if that helps.<o:p></o:p></span></p>
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</blockquote>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:black">-- <br>
Ray Osborn, Senior Scientist<br>
Materials Science Division<br>
Argonne National Laboratory<br>
Argonne, IL 60439, USA<br>
Phone: +1 (630) 252-9011<br>
Email: <a href="mailto:ROsborn@anl.gov">ROsborn@anl.gov</a><o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p align="justify"> </p>
<p align="justify">-- </p>
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