- Timestamp:
- Oct 10, 2009 1:38:08 AM (11 years ago)
- Location:
- 1dwg/trunk/doc
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1dwg/trunk/doc/src/binding_Fortran.xml
r140 r142 15 15 xmlns:xlink="http://www.w3.org/1999/xlink"> 16 16 <title>Fortran binding</title> 17 <bridgehead>18 $Revision$19 $Date$20 </bridgehead>21 17 <para> 22 18 The development of the FORTRAN language, -
1dwg/trunk/doc/src/binding_IgorPro.xml
r140 r142 18 18 <secondary>IgorPro</secondary> 19 19 </indexterm> 20 <bridgehead>21 $Revision$22 $Date$23 </bridgehead>24 20 <para>An import tool (binding) for IgorPro has been created (cansasXML.ipf). You can check out 25 21 the IgorPro working directory from the SVN server (see instructions below). </para> 26 <para>To use the canSASxml.ipf procedure, you must have the XMLutils XOP IGOR plugin installed. 22 <para> 23 To use the <literal>canSASxml.ipf</literal> procedure, 24 you must have the XMLutils XOP IGOR plugin installed. 27 25 See the Usage Notes below. </para> 28 26 <note><para>Note that this tool is not a true … … 83 81 <glossterm>requires</glossterm> 84 82 <glossdef><para> 85 IgorPro: http://www.wavemetrics.com XMLutils - XOP: 86 http://www.igorexchange.com/project/XMLutils (IGOR.5.04.x-1.x-dev, 87 2008-Aug-22) 83 IgorPro: http://www.wavemetrics.com 84 <link xlink:href="http://www.igorexchange.com/project/XMLutils" 85 ><literal 86 >XMLutils XOP</literal></link><footnote><para> 87 <link xlink:href="http://www.igorexchange.com/project/XMLutils" 88 ><literal 89 >http://www.igorexchange.com/project/XMLutils</literal></link> 90 </para></footnote> 91 <indexterm significance="preferred"> 92 <primary>IgorPro package</primary> 93 <secondary>XMLutils XOP</secondary> 94 </indexterm> 95 (minimum requirement: IGOR.5.04.x-1.x-dev, 2008-Aug-22) 88 96 </para></glossdef> 89 97 </glossentry> … … 101 109 <indexterm><primary>XMLutils XOP</primary></indexterm> 102 110 written by Andrew Nelson (ANSTO), 103 is hosted on the IgorExchange. 104 <footnote> 111 is hosted on the IgorExchange.<footnote> 105 112 <para> 106 113 <literal>http://www.igorexchange.com/</literal> … … 109 116 </para> 110 117 <para> One good location to place the checked out XMLutils directory is in the 111 Wavemetrics directory, next to the Igor Pro Folder. 112 <footnote> 118 Wavemetrics directory, next to the Igor Pro Folder.<footnote> 113 119 <para> 114 120 <literal>svn co svn://svn.igorexchange.com/packages/XMLutils/ XMLutils</literal> … … 173 179 <listitem> 174 180 <para> Download cansasXML.ipf. Either checkout from subversion (see above) or, with 175 a web browser, copy cansasXML.ipf from the on-line subversion repository.176 <footnote>181 a web browser, copy cansasXML.ipf from the on-line subversion 182 repository.<footnote> 177 183 <para> 178 184 http://svn.smallangles.net/svn/canSAS/1dwg/trunk/IgorPro/cansasXML.ipf … … 682 688 <section> 683 689 <title>Example test case</title> 684 <para> Here is an example running the test routine <emphasis role="bold" 685 >prjTest_cansas1d()</emphasis>. 686 <programlisting> 690 <para> Here is an example running the test routine <literal>prjTest_cansas1d()</literal>. 691 <programlisting linenumbering="numbered"> 687 692 â¢prjTest_cansas1d() 688 693 XMLopenfile: File(path) to open doesn't exist, or file can't be opened … … 783 788 <link 784 789 xlink:href="http://usaxs.xor.aps.anl.gov/staff/ilavsky/irena.htm" 785 ><emphasis role="bold">Irena</emphasis></link> 786 <footnote> 787 <para>http://usaxs.xor.aps.anl.gov/staff/ilavsky/irena.htm</para> 790 ><emphasis role="bold">Irena</emphasis></link><footnote> 791 <para> 792 <link xlink:href="http://usaxs.xor.aps.anl.gov/staff/ilavsky/irena.htm" 793 ><literal 794 >http://usaxs.xor.aps.anl.gov/staff/ilavsky/irena.htm</literal></link> 795 </para> 788 796 </footnote> 789 <indexterm> 790 <primary>Irena tool suite</primary> 797 <indexterm significance="preferred"> 798 <primary>IgorPro package</primary> 799 <secondary>Irena tool suite</secondary> 791 800 </indexterm> 792 801 tool suite for IgorPro has a GUI to -
1dwg/trunk/doc/src/binding_Java.xml
r140 r142 14 14 version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink"> 15 15 <title>Java JAXB binding</title> 16 <bridgehead>17 $Revision$18 $Date$19 </bridgehead>20 16 <para> 21 17 Documentation for the JAXB binding … … 26 22 is spotty at this time. 27 23 You can check it out with subversion: 28 <programlisting>svn checkout http://svn.smallangles.net/svn/canSAS/1dwg/trunk cansas-1d-standard</programlisting> 24 <example> 25 <title>Check out main trunk using subversion.</title> 26 <programlisting 27 >svn checkout http://svn.smallangles.net/svn/canSAS/1dwg/trunk cansas1d</programlisting> 28 </example> 29 29 (where cansas-1d-standard is a local directory name). 30 30 </para> … … 68 68 <para> 69 69 Here is a Java class that shows how to use the JAXB binding. 70 <indexterm> 71 <primary>Java file</primary> 72 <secondary>JAXB_cansas1d_reader.java</secondary> 73 </indexterm> 70 74 Use this with any of the test data supplied with the cansas-1d-standard directory (above). 71 By default, it shows what is in the <emphasis>1998spheres.xml</emphasis> example file: two samples. 75 By default, it shows the two samples in the <literal>1998spheres.xml</literal> example 76 file.<footnote><para><link 77 xlink:href="http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/1998spheres.xml" 78 ><literal 79 >http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/1998spheres.xml</literal 80 ></link></para></footnote> 81 <indexterm> 82 <primary>XML file</primary> 83 <secondary>1998spheres.xml</secondary> 84 </indexterm> 72 85 (You'll have to get the directory paths right until this documentation improves.) 73 86 </para> … … 79 92 <para> 80 93 Look for the line that has 81 <literal>Qsas[i] = sdt.getIdata().get(i).getQ().getValue();</literal> 82 to see the operations to unwind the data into usable double[] vectors. 94 <informalexample> 95 <programlisting>Qsas[i] = sdt.getIdata().get(i).getQ().getValue();</programlisting> 96 </informalexample> 97 to see the operations that unwind the data into usable double[] vectors. 83 98 Pretty straightforward. 84 99 </para> … … 92 107 <section> 93 108 <title>GetSASdata.java</title> 109 <indexterm> 110 <primary>Java file</primary> 111 <secondary>GetSASdata.java</secondary> 112 </indexterm> 94 113 <programlisting language="java" linenumbering="numbered"><textobject><textdata 95 114 fileref="GetSASdata.java"/></textobject></programlisting> … … 97 116 <section> 98 117 <title>java-test.xml</title> 99 <para> 100 Ok, better to use SVN/TRAC for these files. This example will be improved but it proves the point. 101 </para> 118 <indexterm> 119 <primary>XML file</primary> 120 <secondary>java-test.xml</secondary> 121 </indexterm> 122 <note> 123 <para> 124 Ok, better to use SVN/TRAC for these files. 125 This example could be improved but it proves the point. 126 This file is too long for the manual. 127 </para> 128 </note> 102 129 <programlisting language="xml" linenumbering="numbered"><textobject><textdata 103 130 fileref="java-test.xml"/></textobject></programlisting> -
1dwg/trunk/doc/src/binding_Python.xml
r140 r142 14 14 version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink"> 15 15 <title>Python binding</title> 16 <bridgehead>17 $Revision$18 $Date$19 </bridgehead>20 16 <para> 21 17 Specific <link xlink:href="http://danse.us/trac/sans"><citetitle>support</citetitle></link> … … 32 28 <para> 33 29 Here are some terse instructions to get you started: 34 <programlisting>svn co http://danse.us/trac/sans/browser/trunk/DataLoader DataLoader 30 <example> 31 <title></title> 32 <programlisting 33 >svn co http://danse.us/trac/sans/browser/trunk/DataLoader DataLoader 35 34 cd DataLoader 36 35 python setup.py install</programlisting> 37 The <link xlink:href="http://danse.us/trac/sans/browser/trunk/DataLoader/release_notes.txt"><citetitle>release notes</citetitle></link> have a list of the dependencies. 36 </example> 37 The <link xlink:href="http://danse.us/trac/sans/browser/trunk/DataLoader/release_notes.txt" 38 ><citetitle>release notes</citetitle></link> have a list of the dependencies. 38 39 </para> 39 <section><title>Comments</title> 40 <section> 41 <title>Comments</title> 40 42 <para> 41 43 Other constructive suggestions (that predate the NIST/NCNR support) have been gathered on this page. 42 44 </para> 43 45 </section> 44 <section><title>gnosis.xml.objectify</title> 46 <section> 47 <title>gnosis.xml.objectify</title> 45 48 <para> 46 49 The <link xlink:href="http://freshmeat.net/projects/gnosisxml/">GnosisUtils</link> … … 66 69 You may also need sysAdmin privileges. 67 70 You may need ... 68 <programlisting>cd /tmp 71 <example> 72 <title>Gnosis installation instructions</title> 73 <programlisting linenumbering="numbered" 74 >cd /tmp 69 75 wget http://freshmeat.net/redir/gnosisxml/22028/url_tgz/Gnosis_Utils-1.2.2.tar.gz 70 76 tar xzf Gnosis_Utils-1.2.2.tar.gz 71 77 cd Gnosis_Utils-1.2.2/ 72 78 python setup.py install_all</programlisting> 79 </example> 73 80 </para> 74 81 </section> … … 76 83 <para> 77 84 Here is the Python code (without all that output) 78 (called <emphasis>python-test.py</emphasis>): 79 <programlisting> 80 import gnosis.xml.objectify 85 (called <literal>python-test.py</literal>): 86 <indexterm> 87 <primary>Python file</primary> 88 <secondary>python-test.py</secondary> 89 </indexterm> 90 <example> 91 <title>python-test.py</title> 92 <programlisting linenumbering="numbered" 93 >import gnosis.xml.objectify 81 94 82 95 sasxml = gnosis.xml.objectify.XML_Objectify('bimodal-test1.xml').make_instance() … … 86 99 print sasxml.SASentry.SASdata.Idata[0].Q.unit, sasxml.SASentry.SASdata.Idata[0].I.unit 87 100 print sasxml.SASentry.SASdata.Idata[0].Q.PCDATA, sasxml.SASentry.SASdata.Idata[0].I.PCDATA, sasxml.SASentry.SASdata.Idata[0].Idev.PCDATA</programlisting> 88 </para>89 </section>90 <section>91 <title>execution of that Python code</title>92 <para>93 <programlisting>[Pete@regitte,2441,cansas1dwg-regitte]$ ./python-test.py101 </example> 102 </para> 103 <example> 104 <title>output from <literal>python-test.py</literal></title> 105 <programlisting linenumbering="numbered" 106 >[Pete@regitte,2441,cansas1dwg-regitte]$ ./python-test.py 94 107 SAS bimodal test1 95 108 1992 … … 97 110 1/A 1/cm 98 111 0.0040157139 3497.473 90.72816 99 </programlisting> 100 </para> 101 </section> 102 <section> 112 </programlisting> 113 </example> 114 <example> 103 115 <title>full session output</title> 104 <programlisting>[Pete@regitte,2429,/tmp]$ cd /tmp 116 <programlisting linenumbering="numbered" 117 >[Pete@regitte,2429,/tmp]$ cd /tmp 105 118 /tmp 106 119 [Pete@regitte,2430,/tmp]$ wget http://freshmeat.net/redir/gnosisxml/22028/url_tgz/Gnosis_Utils-1.2.2.tar.gz … … 145 158 >>> print sasxml.SASentry.SASdata.Idata[0].Q.PCDATA, sasxml.SASentry.SASdata.Idata[0].I.PCDATA, sasxml.SASentry.SASdata.Idata[0].Idev.PCDATA 146 159 0.0040157139 3497.473 90.72816</programlisting> 147 </section> 148 <section><title>Conclusion: OK</title> 149 <para> 150 This has the promise of being a useful approach to reading this format in Python.Now, how to write back out... ? 160 </example> 161 </section> 162 <section> 163 <title>Conclusion: OK</title> 164 <para> 165 This has the promise of being a useful approach to reading this format in Python. 166 Now, how to write back out... ? 151 167 </para> 152 168 </section> … … 159 175 Python data structure) for Python from an XML Schema. 160 176 However, the cansas1d/1.0 XML schema (cansas1d.xsd) does not seem to 161 fit the model.It seems, for now, that <emphasis>generateDS-1.12a</emphasis> 162 fails on a certain <emphasis>annotate</emphasis> line. 163 <programlisting>[Pete@regitte,2402,cansas1dwg-regitte]$ python ~/generateDS-1.12a/generateDS.py -p CS1D_ -o cansas1d.py -s cansas1dsubs.py cansas1d.xsd 177 fit the model.It seems, for now, that <literal>generateDS-1.12a</literal> 178 fails on a certain <literal>annotate</literal> line. 179 <programlisting linenumbering="numbered" 180 >[Pete@regitte,2402,cansas1dwg-regitte]$ python ~/generateDS-1.12a/generateDS.py -p CS1D_ -o cansas1d.py -s cansas1dsubs.py cansas1d.xsd 164 181 Traceback (most recent call last): 165 182 File "/home/Pete/generateDS-1.12a/generateDS.py", line 3997, in <module> -
1dwg/trunk/doc/src/bindings.xml
r127 r142 18 18 have been created and contributed. These are listed here by the 19 19 language or software environment.</para> 20 <xi:include href=" cansas1d_binding_Fortran.xml"/>21 <xi:include href=" cansas1d_binding_IgorPro.xml"/>22 <xi:include href=" cansas1d_binding_Java.xml"/>23 <xi:include href=" cansas1d_binding_Python.xml"/>20 <xi:include href="binding_Fortran.xml"/> 21 <xi:include href="binding_IgorPro.xml"/> 22 <xi:include href="binding_Java.xml"/> 23 <xi:include href="binding_Python.xml"/> 24 24 </chapter> -
1dwg/trunk/doc/src/casestudies.xml
r138 r142 13 13 xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xi="http://www.w3.org/2001/XInclude"> 14 14 <title>Case Studies</title> 15 <xi:include href="ca nsas1d_casestudy_collagen.xml"/>16 <xi:include href="ca nsas1d_casestudy_af1410.xml"/>15 <xi:include href="casestudy_collagen.xml"/> 16 <xi:include href="casestudy_af1410.xml"/> 17 17 </section> -
1dwg/trunk/doc/src/casestudy_af1410.xml
r140 r142 14 14 version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink"> 15 15 <title>Case Study: AF1410 steel</title> 16 <bridgehead> $Revision$ $Date$ </bridgehead>17 16 <section> 18 <indexterm significance="preferred">19 <primary>case study</primary>20 <secondary>SANS of AF1410 steel</secondary>21 </indexterm>22 17 <title>Overview</title> 23 18 <note> … … 29 24 </para> 30 25 <para> 26 <indexterm significance="preferred"> 27 <primary>case study</primary> 28 <secondary>SANS of AF1410 steel</secondary> 29 </indexterm> 31 30 The data file contains multiple SASentry elements that pertain to different samples 32 31 treated at different conditions in a time series. Each SASentry element contains two -
1dwg/trunk/doc/src/casestudy_collagen.xml
r140 r142 14 14 version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink"> 15 15 <title>Case Study: Dry Chick Collagen</title> 16 <bridgehead> $Revision$ $Date$ </bridgehead>17 16 <section> 18 17 <title>Overview</title> … … 28 27 Malcolm Capel, NSLS beam line X12C for the sample.) </para> 29 28 <para> 30 < table>31 < title>Figures for dry chick collagen case study</title>29 <informaltable> 30 <!--<title>Figures for dry chick collagen case study</title>--> 32 31 <tgroup cols="2"> 33 32 <tbody> … … 41 40 </imageobject> 42 41 <caption> 43 <para>c ase study: Collagen, SAXS datain Excel table</para>42 <para>collagen SAXS in Excel table</para> 44 43 </caption> 45 44 </mediaobject> … … 53 52 </imageobject> 54 53 <caption> 55 <para>c ase study: Collagen, SAXS data in Excel chart</para>54 <para>collagen SAXS in Excel chart (log-log)</para> 56 55 </caption> 57 56 </mediaobject> … … 60 59 </tbody> 61 60 </tgroup> 62 </ table>61 </informaltable> 63 62 </para> 64 63 <para> The raw data -
1dwg/trunk/doc/src/element_SAScollimation.xml
r140 r142 14 14 version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink"> 15 15 <title>SAScollimation element</title> 16 <bridgehead>17 $Revision$18 $Date$19 </bridgehead>20 16 <itemizedlist mark="opencircle"> 21 17 <listitem> … … 171 167 <title>size</title> 172 168 <para> 173 <table> 174 <title/> 169 <informaltable> 175 170 <tgroup cols='2'> 176 171 <tbody> … … 207 202 </tbody> 208 203 </tgroup> 209 </ table>204 </informaltable> 210 205 <table orient="port" role="small"> 211 206 <title/> -
1dwg/trunk/doc/src/element_SASdata.xml
r141 r142 14 14 version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink"> 15 15 <title>SASdata element</title> 16 <bridgehead> $Revision$ $Date$ </bridgehead>17 16 <itemizedlist mark="opencircle"> 18 17 <indexterm significance="preferred"> -
1dwg/trunk/doc/src/element_SASdetector.xml
r140 r142 14 14 version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink"> 15 15 <title>SASdetector element</title> 16 <bridgehead>17 $Revision$18 $Date$19 </bridgehead>20 16 <itemizedlist mark="opencircle"> 21 17 <indexterm significance="preferred"> … … 204 200 <title>geometry</title> 205 201 <para> 206 <table> 207 <title/> 202 <informaltable> 208 203 <tgroup cols='2'> 209 204 <tbody> … … 249 244 </row> 250 245 </tbody></tgroup> 251 </ table>246 </informaltable> 252 247 </para> 253 248 </section> -
1dwg/trunk/doc/src/element_SASentry.xml
r140 r142 14 14 version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink"> 15 15 <title>SASentry element</title> 16 <bridgehead>17 $Revision$18 $Date$19 </bridgehead>20 16 <itemizedlist mark="opencircle"> 21 17 <listitem> -
1dwg/trunk/doc/src/element_SASinstrument.xml
r140 r142 14 14 version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink"> 15 15 <title>SASinstrument element</title> 16 <bridgehead>17 $Revision$18 $Date$19 </bridgehead>20 16 <itemizedlist mark="opencircle"> 21 17 <listitem> -
1dwg/trunk/doc/src/element_SASnote.xml
r140 r142 14 14 version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink"> 15 15 <title>SASnote element</title> 16 <bridgehead>17 $Revision$18 $Date$19 </bridgehead>20 16 <itemizedlist mark="opencircle"> 21 17 <listitem> -
1dwg/trunk/doc/src/element_SASprocess.xml
r141 r142 14 14 version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink"> 15 15 <title>SASprocess element</title> 16 <bridgehead>17 $Revision$18 $Date$19 </bridgehead>20 16 <itemizedlist mark="opencircle"> 21 17 <listitem> -
1dwg/trunk/doc/src/element_SASroot.xml
r140 r142 14 14 version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink"> 15 15 <title>SASroot element</title> 16 <bridgehead>17 $Revision$18 $Date$19 </bridgehead>20 16 <itemizedlist mark="opencircle"> 21 17 <listitem> -
1dwg/trunk/doc/src/element_SASsample.xml
r140 r142 14 14 version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink"> 15 15 <title>SASsample element</title> 16 <bridgehead>17 $Revision$18 $Date$19 </bridgehead>20 16 <itemizedlist mark="opencircle"> 21 17 <listitem> … … 36 32 <imagedata fileref="../../graphics/3-SASsample.png" width="200pt" scalefit="1"/> 37 33 </imageobject> 38 <textobject>39 <phrase>cansas1d-v1-3-SASsample</phrase>40 </textobject>41 <caption>42 <para>The SASsample element</para>43 </caption>44 34 </mediaobject> 45 35 </figure> … … 177 167 <title>geometry</title> 178 168 <para> 179 <table> 180 <title/> 169 <informaltable> 181 170 <tgroup cols="2"> 182 171 <tbody> … … 215 204 </tbody> 216 205 </tgroup> 217 </ table>206 </informaltable> 218 207 </para> 219 208 </section> -
1dwg/trunk/doc/src/element_SASsource.xml
r140 r142 14 14 version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink"> 15 15 <title>SASsource element</title> 16 <bridgehead> $Revision$ $Date$ </bridgehead>17 16 <itemizedlist mark="opencircle"> 18 17 <listitem> … … 35 34 <phrase>cansas1d-v1-5-SASsource</phrase> 36 35 </textobject> 37 <caption>38 <para>The SASsource element</para>39 </caption>40 36 </mediaobject> 41 37 </figure> 42 <section> 43 <title>SASsource</title> 44 <table orient="port" role="small"> 45 <title/> 46 <tgroup cols="5"> 47 <colspec colname="c1" colwidth="15*"/> 48 <colspec colname="c2" colwidth="15*"/> 49 <colspec colname="c3" colwidth="10*"/> 50 <colspec colname="c4" colwidth="30*"/> 51 <colspec colname="c5" colwidth="30*"/> 52 <tbody> 53 <row> 54 <entry><?dblatex bgcolor="[gray]{0.8}"?>Name</entry> 55 <entry><?dblatex bgcolor="[gray]{0.8}"?>Type</entry> 56 <entry><?dblatex bgcolor="[gray]{0.8}"?>Occurrence</entry> 57 <entry><?dblatex bgcolor="[gray]{0.8}"?>Description</entry> 58 <entry><?dblatex bgcolor="[gray]{0.8}"?>Attributes</entry> 59 </row> 60 <row> 61 <entry> 62 <literal>radiation</literal> 63 <indexterm> 64 <primary>element</primary> 65 <secondary>radiation</secondary> 66 </indexterm> 67 </entry> 68 <entry> string </entry> 69 <entry> [1..1] </entry> 70 <entry> 71 <para> 72 Name of the radiation used. For maximum compatibility with NeXus, 73 use one of the names defined by either <link 74 xlink:href="http://www.nexusformat.org/NXsource" 75 ><citetitle>NeXus</citetitle> 76 <literal>NXsource/type</literal></link> 77 </para> 78 <itemizedlist> 79 <listitem><para>Spallation Neutron Source</para></listitem> 80 <listitem><para>Pulsed Reactor Neutron Source</para></listitem> 81 <listitem><para>Reactor Neutron Source</para></listitem> 82 <listitem><para>Synchrotron X-ray Source</para></listitem> 83 <listitem><para>Pulsed Muon Source</para></listitem> 84 <listitem><para>Rotating Anode X-ray</para></listitem> 85 <listitem><para>Fixed Tube X-ray</para></listitem> 86 </itemizedlist> 87 <para> 88 or <link 89 xlink:href="http://www.nexusformat.org/NXsource" 90 ><citetitle>NeXus</citetitle> 91 <literal>NXsource/probe</literal></link> 92 </para> 93 <itemizedlist> 94 <listitem><para>neutron</para></listitem> 95 <listitem><para>x-ray</para></listitem> 96 <listitem><para>muon</para></listitem> 97 <listitem><para>electron</para></listitem> 98 </itemizedlist> 99 </entry> 100 <entry/> 101 </row> 102 <row> 103 <entry> 104 <literal>beam_size</literal> 105 <indexterm> 106 <primary>element</primary> 107 <secondary>beam_size</secondary> 108 </indexterm> 109 </entry> 110 <entry> container </entry> 111 <entry> [0..1] </entry> 112 <entry> Physical dimension of the beam (incident on the sample). Note: If 113 beam is round, just use X dimension. Note: While Z dimension is allowed 114 by the standard, it does not make sense for small-angle scattering. </entry> 115 <entry><literal>name={name}</literal></entry> 116 </row> 117 <row> 118 <entry> 119 <literal>beam_shape</literal> 120 <indexterm> 121 <primary>element</primary> 122 <secondary>beam_shape</secondary> 123 </indexterm> 124 </entry> 125 <entry> string </entry> 126 <entry> [0..1] </entry> 127 <entry> Text description of the shape of the beam (incident on the sample). </entry> 128 <entry/> 129 </row> 130 <row> 131 <entry> 132 <literal>wavelength</literal> 133 <indexterm> 134 <primary>element</primary> 135 <secondary>wavelength</secondary> 136 </indexterm> 137 </entry> 138 <entry> floating-point number </entry> 139 <entry> [0..1] </entry> 140 <entry> 141 <para> 142 wavelength 143 (<inlineequation> 144 <mathphrase><alt>$\lambda$</alt></mathphrase> 145 </inlineequation>) 146 of radiation incident on the sample. 147 </para> 148 </entry> 149 <entry><literal>unit={unit}</literal></entry> 150 </row> 151 <row> 152 <entry> 153 <literal>wavelength_min</literal> 154 <indexterm> 155 <primary>element</primary> 156 <secondary>wavelength_min</secondary> 157 </indexterm> 158 </entry> 159 <entry> floating-point number </entry> 160 <entry> [0..1] </entry> 161 <entry> Some facilities specify wavelength using a range. The minimum of 162 such a range is given by wavelength_min. </entry> 163 <entry><literal>unit={unit}</literal></entry> 164 </row> 165 <row> 166 <entry> 167 <literal>wavelength_max</literal> 168 <indexterm> 169 <primary>element</primary> 170 <secondary>wavelength_max</secondary> 171 </indexterm> 172 </entry> 173 <entry> floating-point number </entry> 174 <entry> [0..1] </entry> 175 <entry> Some facilities specify wavelength using a range. The maximum of 176 such a range is given by wavelength_max. </entry> 177 <entry><literal>unit={unit}</literal></entry> 178 </row> 179 <row> 180 <entry> 181 <literal>wavelength_spread</literal> 182 <indexterm> 183 <primary>element</primary> 184 <secondary>wavelength_spread</secondary> 185 </indexterm> 186 </entry> 187 <entry> floating-point number </entry> 188 <entry> [0..1] </entry> 189 <entry> Some facilities specify the width of the wavelength spectrum. The 190 width of such a range is given by wavelength_spread. </entry> 191 <entry><literal>unit={unit}</literal></entry> 192 </row> 193 </tbody> 194 </tgroup> 195 </table> 196 </section> 38 <table orient="port" role="small"> 39 <title/> 40 <tgroup cols="5"> 41 <colspec colname="c1" colwidth="15*"/> 42 <colspec colname="c2" colwidth="15*"/> 43 <colspec colname="c3" colwidth="10*"/> 44 <colspec colname="c4" colwidth="30*"/> 45 <colspec colname="c5" colwidth="30*"/> 46 <tbody> 47 <row> 48 <entry><?dblatex bgcolor="[gray]{0.8}"?>Name</entry> 49 <entry><?dblatex bgcolor="[gray]{0.8}"?>Type</entry> 50 <entry><?dblatex bgcolor="[gray]{0.8}"?>Occurrence</entry> 51 <entry><?dblatex bgcolor="[gray]{0.8}"?>Description</entry> 52 <entry><?dblatex bgcolor="[gray]{0.8}"?>Attributes</entry> 53 </row> 54 <row> 55 <entry> 56 <literal>radiation</literal> 57 <indexterm> 58 <primary>element</primary> 59 <secondary>radiation</secondary> 60 </indexterm> 61 </entry> 62 <entry> string </entry> 63 <entry> [1..1] </entry> 64 <entry> 65 <para> 66 Name of the radiation used. For maximum compatibility with NeXus, 67 use one of the names defined by either <link 68 xlink:href="http://www.nexusformat.org/NXsource" 69 ><citetitle>NeXus</citetitle> 70 <literal>NXsource/type</literal></link> 71 </para> 72 <itemizedlist> 73 <listitem><para>Spallation Neutron Source</para></listitem> 74 <listitem><para>Pulsed Reactor Neutron Source</para></listitem> 75 <listitem><para>Reactor Neutron Source</para></listitem> 76 <listitem><para>Synchrotron X-ray Source</para></listitem> 77 <listitem><para>Pulsed Muon Source</para></listitem> 78 <listitem><para>Rotating Anode X-ray</para></listitem> 79 <listitem><para>Fixed Tube X-ray</para></listitem> 80 </itemizedlist> 81 <para> 82 or <link 83 xlink:href="http://www.nexusformat.org/NXsource" 84 ><citetitle>NeXus</citetitle> 85 <literal>NXsource/probe</literal></link> 86 </para> 87 <itemizedlist> 88 <listitem><para>neutron</para></listitem> 89 <listitem><para>x-ray</para></listitem> 90 <listitem><para>muon</para></listitem> 91 <listitem><para>electron</para></listitem> 92 </itemizedlist> 93 </entry> 94 <entry/> 95 </row> 96 <row> 97 <entry> 98 <literal>beam_size</literal> 99 <indexterm> 100 <primary>element</primary> 101 <secondary>beam_size</secondary> 102 </indexterm> 103 </entry> 104 <entry> container </entry> 105 <entry> [0..1] </entry> 106 <entry> Physical dimension of the beam (incident on the sample). Note: If 107 beam is round, just use X dimension. Note: While Z dimension is allowed 108 by the standard, it does not make sense for small-angle scattering. </entry> 109 <entry><literal>name={name}</literal></entry> 110 </row> 111 <row> 112 <entry> 113 <literal>beam_shape</literal> 114 <indexterm> 115 <primary>element</primary> 116 <secondary>beam_shape</secondary> 117 </indexterm> 118 </entry> 119 <entry> string </entry> 120 <entry> [0..1] </entry> 121 <entry> Text description of the shape of the beam (incident on the sample). </entry> 122 <entry/> 123 </row> 124 <row> 125 <entry> 126 <literal>wavelength</literal> 127 <indexterm> 128 <primary>element</primary> 129 <secondary>wavelength</secondary> 130 </indexterm> 131 </entry> 132 <entry> floating-point number </entry> 133 <entry> [0..1] </entry> 134 <entry> 135 <para> 136 wavelength 137 (<inlineequation> 138 <mathphrase><alt>$\lambda$</alt></mathphrase> 139 </inlineequation>) 140 of radiation incident on the sample. 141 </para> 142 </entry> 143 <entry><literal>unit={unit}</literal></entry> 144 </row> 145 <row> 146 <entry> 147 <literal>wavelength_min</literal> 148 <indexterm> 149 <primary>element</primary> 150 <secondary>wavelength_min</secondary> 151 </indexterm> 152 </entry> 153 <entry> floating-point number </entry> 154 <entry> [0..1] </entry> 155 <entry> Some facilities specify wavelength using a range. The minimum of 156 such a range is given by wavelength_min. </entry> 157 <entry><literal>unit={unit}</literal></entry> 158 </row> 159 <row> 160 <entry> 161 <literal>wavelength_max</literal> 162 <indexterm> 163 <primary>element</primary> 164 <secondary>wavelength_max</secondary> 165 </indexterm> 166 </entry> 167 <entry> floating-point number </entry> 168 <entry> [0..1] </entry> 169 <entry> Some facilities specify wavelength using a range. The maximum of 170 such a range is given by wavelength_max. </entry> 171 <entry><literal>unit={unit}</literal></entry> 172 </row> 173 <row> 174 <entry> 175 <literal>wavelength_spread</literal> 176 <indexterm> 177 <primary>element</primary> 178 <secondary>wavelength_spread</secondary> 179 </indexterm> 180 </entry> 181 <entry> floating-point number </entry> 182 <entry> [0..1] </entry> 183 <entry> Some facilities specify the width of the wavelength spectrum. The 184 width of such a range is given by wavelength_spread. </entry> 185 <entry><literal>unit={unit}</literal></entry> 186 </row> 187 </tbody> 188 </tgroup> 189 </table> 197 190 <section> 198 191 <title>beam_size</title> 199 192 <para> 200 <table> 201 <title/> 193 <informaltable> 202 194 <tgroup cols="2"> 203 195 <tbody> … … 230 222 </tbody> 231 223 </tgroup> 232 </ table>224 </informaltable> 233 225 <table orient="port" role="small"> 234 226 <title/> -
1dwg/trunk/doc/src/element_XML_header.xml
r140 r142 14 14 version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink"> 15 15 <title>Required XML Header</title> 16 <bridgehead>17 $Revision$18 $Date$19 </bridgehead>20 16 <example> 21 17 <title>Required header for cansas1d/1.0 XML files</title> -
1dwg/trunk/doc/src/element_any.xml
r131 r142 14 14 version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink"> 15 15 <title><literal>{any}</literal> element</title> 16 <bridgehead>17 $Revision$18 $Date$19 </bridgehead>20 16 <table orient="port" role="small"> 21 17 <title/> … … 50 46 to differentiate them from the canSAS elements in the XML file.) </para> 51 47 </entry> 52 <entry> 53 <para> 54 <emphasis role="bold"> 55 <emphasis>xmlns:{foreign-prefix}</emphasis> 56 </emphasis> ={foreign-namespace} </para> 57 </entry> 48 <entry><literal>xmlns:{foreign-prefix}={foreign-namespace}</literal></entry> 58 49 </row> 59 50 </tbody> -
1dwg/trunk/doc/src/elements.xml
r140 r142 13 13 xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xi="http://www.w3.org/2001/XInclude"> 14 14 <title>Elements of the canSAS XML standard</title> 15 <para>Starting the description of each element will be the current version control 16 <emphasis>Revision</emphasis> and <emphasis>Date</emphasis> of the documentation section. 15 <para> 17 16 There are various elements (tag names) in the cansas1d/1.0 standard. 18 17 Each of these is described below. … … 21 20 <glossentry> 22 21 <glossterm>Name</glossterm> 23 <glossdef><para><emphasis role="italic">Name</emphasis> is the XML tag to be used for this element of the standard.</para></glossdef> 22 <glossdef><para><emphasis role="italic">Name</emphasis> is the XML tag to be 23 used for this element of the standard.</para></glossdef> 24 24 </glossentry> 25 25 <glossentry> … … 107 107 </glosslist> 108 108 109 <xi:include href=" cansas1d_element_XML_header.xml"/>110 <xi:include href=" cansas1d_element_SASroot.xml"/>111 <xi:include href=" cansas1d_element_SASentry.xml"/>112 <xi:include href=" cansas1d_element_SASdata.xml"/>113 <xi:include href=" cansas1d_element_SASsample.xml"/>114 <xi:include href=" cansas1d_element_SASinstrument.xml"/>115 <xi:include href=" cansas1d_element_SASsource.xml"/>116 <xi:include href=" cansas1d_element_SAScollimation.xml"/>117 <xi:include href=" cansas1d_element_SASdetector.xml"/>118 <xi:include href=" cansas1d_element_SASprocess.xml"/>119 <xi:include href=" cansas1d_element_SASnote.xml"/>120 <xi:include href=" cansas1d_element_any.xml"/>109 <xi:include href="element_XML_header.xml"/> 110 <xi:include href="element_SASroot.xml"/> 111 <xi:include href="element_SASentry.xml"/> 112 <xi:include href="element_SASdata.xml"/> 113 <xi:include href="element_SASsample.xml"/> 114 <xi:include href="element_SASinstrument.xml"/> 115 <xi:include href="element_SASsource.xml"/> 116 <xi:include href="element_SAScollimation.xml"/> 117 <xi:include href="element_SASdetector.xml"/> 118 <xi:include href="element_SASprocess.xml"/> 119 <xi:include href="element_SASnote.xml"/> 120 <xi:include href="element_any.xml"/> 121 121 </section> -
1dwg/trunk/doc/src/examples.xml
r140 r142 10 10 ########### SVN repository information ################### 11 11 --> 12 < chapterxml:id="wiki-other" xmlns="http://docbook.org/ns/docbook" version="5.0"12 <appendix xml:id="wiki-other" xmlns="http://docbook.org/ns/docbook" version="5.0" 13 13 xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xi="http://www.w3.org/2001/XInclude"> 14 <title> Other matters</title>14 <title>Examples</title> 15 15 <para>Various topics have been considered or presented in considering this standard. Some are 16 16 described below.</para> 17 <xi:include href="cansas1d_definition_of_terms.xml"/> 18 <xi:include href="xml-help.xml"/> 19 <section xml:id="the_intensity_problem"> 20 <title>The Intensity Problem</title> 21 <para> The intensity (see 22 <link 23 xlink:href="#cansas1d_documentation-element-SASdata" 24 ><literal>SASdata/Idata</literal></link>) 25 is permitted in three different forms: </para> 26 <itemizedlist> 27 <listitem> 28 <para><emphasis role="bold">absolute units:</emphasis> differential cross-section 29 per unit volume per unit solid angle (typical unit: 1/cm)</para> 30 </listitem> 31 <listitem> 32 <para><emphasis role="bold">absolute units:</emphasis> differential cross-section 33 per unit atom per unit solid angle (typical unit: cm^2)</para> 34 </listitem> 35 <listitem> 36 <para><emphasis role="bold">arbitrary units:</emphasis> usually a ratio of two 37 detectors but unit is meaningless (typical unit: a.u.)</para> 38 </listitem> 39 </itemizedlist> 40 <para> This presents a few problems 41 <indexterm> 42 <primary>intensity</primary> 43 <secondary>problem</secondary> 44 </indexterm> 45 <indexterm> 46 <primary>intensity</primary> 47 <secondary>absolute</secondary> 48 </indexterm> 49 for analysis software to sort out when reading the data. 50 Fortunately, it is possible to analyze the unit attribute to decide which type of 51 intensity is being reported and make choices at the time the file is read. But this is 52 an area for consideration and possible improvement. </para> 53 <para> One problem arises with software that automatically converts data into some canonical 54 units used by that software. The software should not convert units between these three 55 types of intensity indiscriminately. </para> 56 <para> A second problem is that when arbitrary units are used, then the set of possible 57 analytical results is restricted (such as no meaningful volume fraction or number 58 density can be determined directly from I(Q)). </para> 59 </section> 17 <!-- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ --> 18 <!-- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ --> 60 19 <section xml:id="xml-data-file"> 61 20 <title>Example XML Data Files</title> … … 73 32 <section xml:id="data-simple"> 74 33 <title>data-simple.xml</title> 75 <para>The example data file <literal>data-simple.xml</literal> shows 76 just the basic elements of the cansas1d/1.0 standard. Only a single data 77 point has been shown to more clearly show the other structure. 34 <para> 35 The example data file <literal>data-simple.xml</literal> 36 <indexterm> 37 <primary>XML file</primary> 38 <secondary>data-simple.xml</secondary> 39 </indexterm> 40 shows just the basic elements of the cansas1d/1.0 standard. Only a 41 single data point has been shown to more clearly show the other structure. 78 42 The data file is actually an excerpt from the 79 43 <link … … 90 54 <secondary>cansas1d/1.0 data file</secondary> 91 55 </indexterm> 92 <programlisting language="xml" linenumbering="numbered"> 93 <textobject> 94 <textdata fileref="data-simple.xml"/> 95 </textobject> 96 </programlisting> 56 <example> 57 <title><citetitle>data-simple.xml</citetitle></title> 58 <programlisting language="xml" linenumbering="numbered"> 59 <textobject> 60 <textdata fileref="data-simple.xml"/> 61 </textobject> 62 </programlisting> 63 </example> 97 64 </section> 98 65 <section xml:id="data-cansas1d"> 99 66 <title>cansas1d.xml</title> 100 67 <para> 101 The example data file <literal>cansas1d.xml</literal> shows example 68 The example data file <literal>cansas1d.xml</literal> 69 <indexterm> 70 <primary>XML file</primary> 71 <secondary>cansas1d.xml</secondary> 72 </indexterm> 73 shows example 102 74 of most of the elements of the cansas1d/1.0 standard. Only a single data 103 75 point has been shown to more clearly show the other structure. … … 110 82 <secondary>cansas1d/1.0 data file</secondary> 111 83 </indexterm> 112 <programlisting language="xml" linenumbering="numbered"> 113 <textobject> 114 <textdata fileref="../../cansas1d.xml"/> 115 </textobject> 116 </programlisting> 84 <example> 85 <title><citetitle>cansas1d.xml</citetitle></title> 86 <programlisting language="xml" linenumbering="numbered"> 87 <textobject> 88 <textdata fileref="../../cansas1d.xml"/> 89 </textobject> 90 </programlisting> 91 </example> 117 92 </section> 118 93 </section> … … 198 173 </section> 199 174 </section> 200 </ chapter>175 </appendix> -
1dwg/trunk/doc/src/glossary.xml
r140 r142 11 11 --> 12 12 <!-- from: http://www.smallangles.net/wgwiki/index.php/cansas1d_cansas1d_definition_of_terms--> 13 < section13 <appendix 14 14 xml:id="cansas1d_documentation-element-cansas1d_definition_of_terms" 15 15 xmlns="http://docbook.org/ns/docbook" … … 17 17 xmlns:xlink="http://www.w3.org/1999/xlink"> 18 18 <title>Glossary</title> 19 <bridgehead>20 $Revision$21 $Date$22 </bridgehead>23 19 <note> 24 <para> 20 <para>This Glossary 25 21 might not be provided in future versions of this manual. </para></note> 26 22 <para> … … 28 24 <indexterm><primary>glossary</primary></indexterm> 29 25 defining the details about each specific field (XPath string, 30 XML elements and attributes) in the cansas1d/1.0 standard.<indexterm><primary>cansas1d/1.0 standard</primary></indexterm> 26 XML elements and attributes) in the cansas1d/1.0 standard. 27 <indexterm><primary>cansas1d/1.0 standard</primary></indexterm> 31 28 </para> 32 29 <itemizedlist mark="opencircle"><listitem> … … 105 102 </itemizedlist> 106 103 <glossary> 107 <title>Glossary</title> 104 <title>Listed by full XPath reference</title> 105 <subtitle>assumes namespace declaration: <literal>xmlns:cs="cansas1d/1.0"</literal></subtitle> 108 106 <glosslist> 109 107 <glossentry> … … 1069 1067 </glosslist> 1070 1068 </glossary> 1071 </ section>1069 </appendix> -
1dwg/trunk/doc/src/manual.xml
r138 r142 32 32 </author> 33 33 <!--<edition>$Id$</edition>--> 34 < edition>draft</edition>34 <!--<edition>draft</edition>--> 35 35 <pubdate>2009</pubdate> 36 36 <legalnotice> … … 55 55 56 56 <xi:include href="preface.xml"/> 57 <xi:include href=" wiki.xml"/>57 <xi:include href="overview.xml"/> 58 58 <xi:include href="specification.xml"/> 59 59 <xi:include href="tutorial.xml"/> 60 60 <xi:include href="bindings.xml"/> 61 <xi:include href="other.xml"/> 62 <!--<xi:include href="appendices.xml"/>--> 61 <!-- +++++ appendices +++++ --> 62 <xi:include href="intensity-problem.xml"/> 63 <xi:include href="examples.xml"/> 64 <xi:include href="glossary.xml"/> 65 <xi:include href="xml-help.xml"/> 63 66 <index/> 64 67 </book> -
1dwg/trunk/doc/src/overview.xml
r140 r142 21 21 forum of users, software developers, and facility staff was to discuss 22 22 better sharing of SAS data analysis software. The <link 23 xlink:href="http://www.smallangles.net/canSAS">canSAS</link> 24 <footnote><para> 23 xlink:href="http://www.smallangles.net/canSAS">canSAS</link><footnote><para> 25 24 <link xlink:href="http://www.smallangles.net/canSAS" 26 25 ><literal>http://www.smallangles.net/canSAS</literal></link></para></footnote> … … 81 80 <link 82 81 xlink:href="http://www.smallangles.net/wgwiki/index.php/1D_Data_Formats_Working_Group" 83 >canSAS 1D Data Formats Working Group</link> 84 <footnote> 82 >canSAS 1D Data Formats Working Group</link><footnote> 85 83 <para> 86 84 <link xlink:href="http://www.smallangles.net/wgwiki/index.php/1D_Data_Formats_Working_Group" … … 91 89 <link 92 90 xlink:href="http://www.smallangles.net/wgwiki/index.php/Talk:1D_Data_Formats_Working_Group" 93 >discussion</link> 94 <footnote> 91 >discussion</link><footnote> 95 92 <para> 96 93 <link xlink:href="http://www.smallangles.net/wgwiki/index.php/Talk:1D_Data_Formats_Working_Group" … … 317 314 </listitem> 318 315 <listitem> 319 <para> units to be given in standard SI abbreviations (eg, m, cm, mm, nm, K) 316 <para> 317 units 318 <indexterm significance="preferred"> 319 <primary>unit</primary> 320 </indexterm> 321 <indexterm> 322 <primary>units</primary> 323 <see>unit</see> 324 </indexterm> 325 to be given in standard SI abbreviations (eg, m, cm, mm, nm, K) 320 326 with the following exceptions: </para> 321 327 <orderedlist numeration="loweralpha"> … … 382 388 <secondary>rotation</secondary> 383 389 </indexterm> 384 < table>385 < title/>390 <informaltable> 391 <!--<title/>--> 386 392 <tgroup cols="2"> 387 393 <tbody> … … 414 420 </tbody> 415 421 </tgroup> 416 </ table>422 </informaltable> 417 423 </para> 418 424 </figure> … … 437 443 <listitem> 438 444 <para> Unicode characters MUST NOT be used</para> 445 <note><para>Perhaps this could be relaxed in v1.1?</para></note> 439 446 </listitem> 440 447 <listitem> … … 481 488 <para>The translation and orientation geometry definitions used here are different than 482 489 those used by <link xlink:href="http://www.nanotech.wisc.edu/shadow" 483 ><literal>SHADOW</literal></link> 484 <footnote><para> 490 ><literal>SHADOW</literal></link><footnote><para> 485 491 <link xlink:href="http://www.nanotech.wisc.edu/shadow" 486 492 ><literal>http://www.nanotech.wisc.edu/shadow</literal></link></para></footnote> … … 493 499 <para>The 494 500 <link xlink:href="http://www.smallangles.net/canSAS/xmlWriter/" 495 ><emphasis role="italic">canSAS/xmlWriter</emphasis></link> 496 <footnote> 501 ><emphasis role="italic">canSAS/xmlWriter</emphasis></link><footnote> 497 502 <para><link xlink:href="http://www.smallangles.net/canSAS/xmlWriter/" 498 503 ><literal>http://www.smallangles.net/canSAS/xmlWriter/</literal></link></para> … … 506 511 ...). </para> 507 512 <para>Press the <code>Submit</code> button and you will receive a nicely 508 formatted WWW page with the SAS data. If you then choose "View page source" (from509 one of your browser menus), you will see the raw XML of the cansas1d/1.0 XML format513 formatted WWW page with the SAS data. If you then choose <emphasis>View page source</emphasis> 514 (from one of your browser menus), you will see the raw XML of the cansas1d/1.0 XML format 510 515 and you can copy/paste this into an XML file. </para> 511 516 <para>The SAS data that you paste into the form box is likely to be copied directly from … … 523 528 ><literal>cansas1d.xsd</literal></link> 524 529 <link xlink:href="http://www.w3schools.com/xsd" 525 >XML Schema</link> 526 <footnote><para> 530 >XML Schema</link><footnote><para> 527 531 <link xlink:href="http://www.w3schools.com/xsd" 528 532 ><literal>http://www.w3schools.com/xsd</literal></link></para></footnote> 529 533 <indexterm><primary>XML Schema</primary></indexterm> 530 defines the rules for the XML file format 531 <footnote> 534 defines the rules for the XML file format<footnote> 532 535 <para> 533 536 TRAC: … … 535 538 ><literal>http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/cansas1d.xsd</literal></link> 536 539 </para> 537 </footnote> 538 <footnote> 540 </footnote><footnote> 539 541 <para> 540 542 SVN: … … 549 551 <title>XML Stylesheets</title> 550 552 <para> 551 XML stylesheets (also known as XSLT) 552 <footnote> 553 XML stylesheets (also known as XSLT)<footnote> 553 554 <para> 554 555 <link xlink:href="http://www.w3schools.com/xsl/" … … 559 560 </indexterm> 560 561 can be used to extract metadata or to convert into another file format. The 561 default canSAS stylesheet <literal>cansasxml-html.xsl</literal> 562 <footnote> 562 default canSAS stylesheet <literal>cansasxml-html.xsl</literal><footnote> 563 563 <para> 564 564 <link xlink:href="http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansasxml-html.xsl" … … 569 569 (such as Firefox or Internet Explorer) or to import into Microsoft Excel 570 570 (with the added XML support in Excel). (See the excellent write-up by Steve 571 King, ISIS, 572 <footnote> 571 King, ISIS,<footnote> 573 572 <para> 574 573 <link xlink:href="http://www.isis.rl.ac.uk/archive/LargeScale/LOQ/xml/cansas_xml_format.pdf" … … 583 582 </section> 584 583 <section xml:id="cansas1d_documentation-programming_suggestions"> 585 <title>Suggestions for support software that write scansas1d/1.0 XML data files</title>584 <title>Suggestions for support software that write cansas1d/1.0 XML data files</title> 586 585 <para> 587 586 Some common best practices have been identified in the list below. … … 613 612 <listitem> 614 613 <para>The most recent XSLT file can be identified by examining the file 615 for the <literal>$ Revision: </literal> string. For example: 616 <code># $Revision: 111 $</code> is version 111. </para> 614 for the <literal>$ Revision: </literal> string such as in the next example. 615 <informalexample> 616 <programlisting># $Revision: 111 $</programlisting> 617 </informalexample> 618 </para> 617 619 </listitem> 618 620 </itemizedlist> … … 623 625 <listitem> 624 626 <para> 625 Basic example: 626 <footnote><para> 627 Basic example:<footnote><para> 627 628 <link xlink:href="http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/cansas1d.xml" 628 ><literal>http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/cansas1d.xml</literal></link></para></footnote> 629 ><literal 630 >http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/cansas1d.xml</literal 631 ></link></para></footnote> 632 <indexterm> 633 <primary>XML file</primary> 634 <secondary>cansas1d.xml</secondary> 635 </indexterm> 629 636 Note that, for clarity, only one row of data is 630 637 shown. This is probably a very good example to use as a starting point for … … 633 640 <listitem> 634 641 <para> 635 Bimodal test data: 636 <footnote><para> 642 Bimodal test data:<footnote><para> 637 643 <link xlink:href="http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/bimodal-test1.xml" 638 ><literal>http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/bimodal-test1.xml</literal></link></para></footnote> 639 Simulated SAS data (with added noise) calculated from model bimodal size distribution to test size distribution analysis routines.</para> 640 </listitem> 641 <listitem> 642 <para> 643 Glassy Carbon Round Robin: 644 <footnote> 644 ><literal 645 >http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/bimodal-test1.xml</literal 646 ></link></para></footnote> 647 <indexterm> 648 <primary>XML file</primary> 649 <secondary>bimodal-test1.xml</secondary> 650 </indexterm> 651 <indexterm> 652 <primary>case study</primary> 653 <secondary>bimodal test data</secondary> 654 </indexterm> 655 Simulated SAS data (with added noise) calculated from model bimodal size 656 distribution to test size distribution analysis routines.</para> 657 </listitem> 658 <listitem> 659 <para> 660 Glassy Carbon Round Robin:<footnote> 645 661 <para> 646 662 <link xlink:href="http://www.smallangles.net/wgwiki/index.php/Glassy_Carbon_Round_Robin" … … 648 664 ></link></para> 649 665 </footnote> 666 <indexterm> 667 <primary>case study</primary> 668 <secondary>glassy carbon round robin</secondary> 669 </indexterm> 650 670 Samples of a commercial glassy carbon 651 671 measured at several facilities worldwide.</para> … … 655 675 <link xlink:href="#cansas1d_documentation-case_study-collagen" 656 676 >dry chick collagen</link> 677 <indexterm> 678 <primary>case study</primary> 679 <secondary>SAXS of dry chick collagen</secondary> 680 </indexterm> 657 681 illustrates the 658 682 minimum information necessary to meet the requirements of the standard … … 662 686 <para>SANS data from 663 687 <link xlink:href="#cansas1d_documentation-case_study-af1410" 664 >AF1410 steel</link>: 665 <footnote><para> 666 <link xlink:href="http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/examples/af1410/" 667 ><literal>http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/examples/af1410/</literal 668 ></link></para></footnote> 688 >AF1410 steel</link>:<footnote><para> 689 <link xlink:href="http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/examples/af1410/" 690 ><literal>http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/examples/af1410/</literal 691 ></link></para></footnote> 692 <indexterm> 693 <primary>case study</primary> 694 <secondary>SANS of AF1410 steel</secondary> 695 </indexterm> 669 696 SANS study using magnetic 670 697 contrast variation (with multiple samples and multiple data sets for each … … 673 700 <listitem> 674 701 <para> 675 <literal>cansas1d-template.xml</literal>: 676 <footnote><para> 702 <literal>cansas1d-template.xml</literal>:<footnote><para> 677 703 <link xlink:href="http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/cansas1d-template.xml" 678 ><literal>http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/cansas1d-template.xml</literal></link></para></footnote> 704 ><literal 705 >http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/cansas1d-template.xml</literal 706 ></link></para></footnote> 707 <indexterm> 708 <primary>XML file</primary> 709 <secondary>cansas1d-template.xml</secondary> 710 </indexterm> 679 711 This is used to test all the rules in the XML 680 712 Schema. This is probably not a very good example to use as a starting point … … 686 718 <title>XML layout for multiple experiments</title> 687 719 <para>Each experiment is described with a single <literal>SASentry</literal> element. The 688 fragment below shows how multiple experiments can be included in a single XML 720 fragment below shows how multiple experiments 721 <indexterm> 722 <primary>multiple experiments</primary> 723 </indexterm> 724 <indexterm> 725 <primary>multiple data sets</primary> 726 </indexterm> 727 can be included in a single XML 689 728 file. Full examples of canSAS XML files with multiple experiments 690 729 include:</para> 691 730 <itemizedlist> 692 731 <listitem> 693 <para> ISIS LOQ SANS instrument: 694 <footnote><para> 695 <link xlink:href="http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/W1W2.XML" 696 ><literal>http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/W1W2.XML</literal></link></para></footnote> 732 <para> ISIS LOQ SANS instrument:<footnote><para> 733 <link xlink:href="http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/W1W2.XML" 734 ><literal 735 >http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/W1W2.XML</literal 736 ></link></para></footnote> 737 <indexterm> 738 <primary>XML file</primary> 739 <secondary>W1W2.XML</secondary> 740 </indexterm> 697 741 multiple data sets. 698 742 </para> 699 743 </listitem> 700 744 <listitem> 701 <para> AF1410 steel SANS contrast variation study from NIST: 702 <footnote><para> 745 <para> AF1410 steel SANS contrast variation study from NIST:<footnote><para> 703 746 <link xlink:href="http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/examples/af1410/cs_af1410.xml" 704 ><literal>http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/examples/af1410/cs_af1410.xml</literal></link></para></footnote> 747 ><literal 748 >http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/examples/af1410/cs_af1410.xml</literal 749 ></link></para></footnote> 750 <indexterm> 751 <primary>XML file</primary> 752 <secondary>cs_af1410.xml</secondary> 753 </indexterm> 705 754 SANS study using magnetic 706 755 contrast variation (with multiple samples and multiple data sets for each … … 711 760 <para>Here is a brief sketch of how a file would be arranged with multiple SASentry 712 761 elements and multiple SASdata elements. 762 <indexterm> 763 <primary>XML file</primary> 764 <secondary>brief-sketch-multiple.xml</secondary> 765 </indexterm> 713 766 <example> 714 767 <title>Brief sketch of a file with multiple SASentry and SASdata blocks.</title> … … 725 778 <title>Foreign Elements</title> 726 779 <para> To allow for inclusion of elements that are not defined by the 727 780 <literal>cansas1d.xsd</literal> XML 728 781 Schema, XML <emphasis role="italic">foreign elements</emphasis> 729 782 <indexterm> … … 735 788 <link xlink:href="#wiki-XML_Help"><emphasis>XML Help</emphasis></link> 736 789 for more help with XML foreign elements. </para> 737 <para> There is one example that demonstrates the use of a foreign namespace: 738 <footnote> 790 <para> 791 There is an example that demonstrates the use of a foreign 792 namespace:<footnote> 739 793 <para> 740 794 <link 741 795 xlink:href="http://svn.smallangles.net/trac/canSAS/browser/1dwg/data/Glassy%20Carbon/ISIS/GLASSYC_C4G8G9_withTL.xml" 742 ><literal>http://svn.smallangles.net/trac/canSAS/browser/1dwg/data/Glassy%20Carbon/ISIS/GLASSYC_C4G8G9_withTL.xml</literal></link></para> 796 ><literal 797 >http://svn.smallangles.net/trac/canSAS/browser/1dwg/data/Glassy%20Carbon/ISIS/GLASSYC_C4G8G9_withTL.xml</literal></link></para> 743 798 </footnote> 744 799 This example uses a foreign namespace to record the transmission spectra related to 745 the acquisition of the SANS data at a time-of-flight facility. Look for the 746 <code><transmission_spectrum xmlns="urn:transmission:spectrum"></code> 747 element at line 153. The foreign namespace given 748 (<literal>urn:transmission:spectrum</literal>) becomes the default for just the 749 <literal>transmission_spectrum</literal> element. </para> 750 <para> Also refer to <link 751 xlink:href="http://svn.smallangles.net/trac/canSAS/changeset/47">canSAS TRAC 752 ticket #47</link> for an example of arranging the content in 800 the acquisition of the SANS data at a time-of-flight facility. Look near line 153 801 for the element om the next example. 802 <informalexample> 803 <programlisting><transmission_spectrum xmlns="urn:transmission:spectrum"></programlisting> 804 </informalexample> 805 The foreign namespace given 806 (<literal>urn:transmission:spectrum</literal>) becomes the default namespace for just the 807 <literal>transmission_spectrum</literal> element. </para> 808 <para>Also refer to <link 809 xlink:href="http://svn.smallangles.net/trac/canSAS/changeset/47">canSAS TRAC 810 ticket #47</link> for an example of arranging the content in 753 811 <literal>SASprocessnote</literal> to avoid the use of foreign namespace 754 812 elements. </para> … … 787 845 </indexterm> 788 846 <indexterm> 789 <primary> FORTRAN</primary>790 <see>binding, FORTRAN</see>847 <primary>IgorPro</primary> 848 <see>binding, IgorPro</see> 791 849 </indexterm> 792 850 </para> … … 827 885 >ISIS LOQ instrument</link> has provided an <link 828 886 xlink:href="http://www.isis.rl.ac.uk/archive/LargeScale/LOQ/xml/cansas_xml_format.pdf" 829 >excellent description</link> 830 <footnote><para><link 887 >excellent description</link><footnote><para><link 831 888 xlink:href="http://www.isis.stfc.ac.uk/instruments/loq/loq2470.html" 832 889 ><literal>http://www.isis.stfc.ac.uk/instruments/loq/loq2470.html</literal … … 837 894 <link 838 895 xlink:href="http://www.isis.rl.ac.uk/archive/LargeScale/LOQ/loq.htm">old 839 WWW site</link> 840 <footnote><para><link 896 WWW site</link><footnote><para><link 841 897 xlink:href="http://www.isis.rl.ac.uk/LargeScale/LOQ/loq.htm" 842 898 ><literal>http://www.isis.rl.ac.uk/LargeScale/LOQ/loq.htm</literal … … 851 907 ><emphasis role="italic">canSAS/xmlWriter</emphasis></link> 852 908 <indexterm><primary><literal>xmlWriter</literal></primary></indexterm> 853 is implemented in <link xlink:href="http://www.php.net">PHP</link >854 <footnote><para><link xlink:href="http://www.php.net"909 is implemented in <link xlink:href="http://www.php.net">PHP</link 910 ><footnote><para><link xlink:href="http://www.php.net" 855 911 ><literal>http://www.php.net</literal></link></para></footnote> 856 912 <indexterm> … … 865 921 (<link 866 922 xlink:href="http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/php/xmlWriter/index.php" 867 >PHP source</link>) 868 <footnote> 923 >PHP source</link>)<footnote> 869 924 <para> 870 925 <link xlink:href="http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/php/xmlWriter/index.php" … … 872 927 </para> 873 928 </footnote> 874 The code uses <link xlink:href="http://www.php.net/DomDocument">DomDocument</link >875 <footnote><para><link xlink:href="http://www.php.net/DomDocument"929 The code uses <link xlink:href="http://www.php.net/DomDocument">DomDocument</link 930 ><footnote><para><link xlink:href="http://www.php.net/DomDocument" 876 931 ><literal>http://www.php.net/DomDocument</literal></link></para></footnote> 877 932 to build the XML file. Look for the line beginning with … … 931 986 <section xml:id="cansas1d_documentation-schema_validation"> 932 987 <title>Validation of XML against the Schema</title> 988 <indexterm> 989 <primary>validation</primary> 990 <secondary>against XML Schema</secondary> 991 </indexterm> 933 992 <orderedlist> 934 993 <listitem> … … 946 1005 <listitem> 947 1006 <para>paste content of 948 <literal>cansas1d.xsd</literal> 949 <footnote><para><link 1007 <literal>cansas1d.xsd</literal><footnote><para><link 950 1008 xlink:href="http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" 951 1009 ><literal>http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd</literal -
1dwg/trunk/doc/src/preface.xml
r134 r142 22 22 canSAS 1-D Data Format, v1.0 23 23 </para> 24 < note><para>24 <!--<note><para> 25 25 Provide a note here describing canSAS and the initiative to establish 26 26 a standard file format. Note that the cansas1d/1.0 XML data files must adhere to the 27 27 XML rules which includes being well-formed 28 28 <indexterm><primary>XML</primary><secondary>well-formed</secondary></indexterm> 29 (including the use of closing tags). 30 <footnote> 29 (including the use of closing tags).<footnote> 31 30 <para> 32 31 For example, see … … 44 43 ><literal>cansas1d.xsd</literal> </link> 45 44 are deemed to be valid cansas1d/1.0 data files. 46 </para></note> 45 </para></note>--> 47 46 <para> 48 47 The name <emphasis role="italic">canSAS</emphasis> … … 71 70 <link 72 71 xlink:href="http://www.smallangles.net/wgwiki/index.php/Talk:1D_Data_Formats_Working_Group" 73 >discussion</link> 74 <footnote><para><link 72 >discussion</link><footnote><para><link 75 73 xlink:href="http://www.smallangles.net/wgwiki/index.php/Talk:1D_Data_Formats_Working_Group" 76 74 ><literal>http://www.smallangles.net/wgwiki/index.php/Talk:1D_Data_Formats_Working_Group</literal></link></para></footnote> … … 85 83 <link 86 84 xlink:href="http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/cansas1d.xsd" 87 >cansas1d/1.0 SAS XML Schema</link> 88 <footnote><para><link 85 >cansas1d/1.0 SAS XML Schema</link><footnote><para><link 89 86 xlink:href="http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/cansas1d.xsd" 90 87 ><literal>http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/cansas1d.xsd</literal></link></para></footnote> -
1dwg/trunk/doc/src/specification.xml
r140 r142 66 66 with <literal>analysis</literal> and the element might look like this: 67 67 <informalexample> 68 <programlisting> 69 <analysis> 70 ... analysis content goes here ... 71 </analysis> 68 <programlisting><analysis> 69 ... analysis content goes here ... 70 </analysis> 72 71 </programlisting> 73 72 </informalexample> -
1dwg/trunk/doc/src/test.xml
r132 r142 52 52 </info> 53 53 54 <xi:include href=" wiki.xml"/>54 <xi:include href="overview.xml"/> 55 55 56 56 <index/> -
1dwg/trunk/doc/src/tutorial.xml
r138 r142 20 20 scattering data in XML files. 21 21 </para> 22 <note><para>More needs to be written here.</para></note> 22 <para>At present, the tutorial section consists of two case studies, 23 which can serve as examples. The opportunity is ripe for a 24 better tutorial.</para> 23 25 24 26 <xi:include href="casestudies.xml"/> -
1dwg/trunk/doc/src/xml-help.xml
r134 r142 10 10 ########### SVN repository information ################### 11 11 --> 12 < sectionxml:id="wiki-XML_Help" xmlns="http://docbook.org/ns/docbook" version="5.0"12 <appendix xml:id="wiki-XML_Help" xmlns="http://docbook.org/ns/docbook" version="5.0" 13 13 xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xi="http://www.w3.org/2001/XInclude"> 14 14 <title>XML Help</title> … … 114 114 </listitem> 115 115 </itemizedlist> 116 </ section>116 </appendix>
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