Changeset 129
- Timestamp:
- Oct 2, 2009 5:47:47 PM (10 years ago)
- Location:
- 1dwg/trunk/doc
- Files:
-
- 3 added
- 7 edited
Legend:
- Unmodified
- Added
- Removed
-
1dwg/trunk/doc/src/cansas1d_binding_Python.xml
r127 r129 39 39 <section><title>gnosis.xml.objectify</title> 40 40 <para> 41 The GnosisUtils (http://freshmeat.net/projects/gnosisxml/) offer a method to readany XML file into Python data structures. This utility does not validate the XML against aspecific XML Schema which can be both good (flexible, especially when XML Foreign Namespace elements are used) and not so good (XML content not guaranteed to be <emphasis>by the rules</emphasis>). 41 The <link xlink:href="http://freshmeat.net/projects/gnosisxml/">GnosisUtils</link> 42 <footnote><para>http://freshmeat.net/projects/gnosisxml/</para></footnote> 43 offer a method to read any XML file into Python data structures. This utility 44 does not validate the XML against a specific XML Schema which can be both good 45 (flexible, especially when XML Foreign Namespace elements are used) and not 46 so good (XML content not guaranteed to be valid <emphasis>by the rules</emphasis>). 42 47 </para> 43 48 <para> 44 A quick test of this turned up an acceptable result in that it was able to read several of the canSAS test XML files, including those with foreign namespaces.And <emphasis role="bold"><emphasis>it was very easy.</emphasis></emphasis> (Especially with some help from http://www.xml.com/pub/a/2003/07/02/py-xml.html) 49 A quick test of this turned up an acceptable result in that it was able to read 50 several of the canSAS test XML files, including those with foreign namespaces. 51 And <emphasis role="bold"><emphasis> it was very easy.</emphasis></emphasis> 52 (Especially with some help from http://www.xml.com/pub/a/2003/07/02/py-xml.html) 45 53 </para> 46 54 <para> … … 49 57 <section><title>installation</title> 50 58 <para> 51 Here is the condensed installation (without all that output) steps. Your system may have gnosis already installed. You may also need sysAdmin privileges. You may need ... 59 Here is the condensed installation (without all that output) steps. 60 Your system may have gnosis already installed. 61 You may also need sysAdmin privileges. 62 You may need ... 52 63 <programlisting>cd /tmp 53 64 wget http://freshmeat.net/redir/gnosisxml/22028/url_tgz/Gnosis_Utils-1.2.2.tar.gz -
1dwg/trunk/doc/src/cansas1d_definition_of_terms.xml
r127 r129 21 21 $Date$ 22 22 </bridgehead> 23 <note> <para>24 This Definition of Terms may not be provided in future versions of this manual.25 </para></note>23 <note> 24 <para> This Definition of Terms 25 may not be provided in future versions of this manual. </para></note> 26 26 <para> 27 Note: 27 This section provides a glossary 28 <indexterm><primary>glossary</primary></indexterm> 29 <indexterm><primary>definition of terms</primary></indexterm> 30 defining the details about each specific field (XPath string, 31 XML elements and attributes) in the cansas1d/1.0 standard.<indexterm><primary>cansas1d/1.0 standard</primary></indexterm> 28 32 </para> 29 33 <itemizedlist mark="opencircle"><listitem> … … 107 111 <glossterm><code>/cs:SASroot</code></glossterm> 108 112 <glossdef><para> 109 [1..1] The canSAS reduced 1-D SAS data will be in the SASroot database. This is similar to NXroot used by NeXus. 113 [1..1] The canSAS reduced 1-D SAS data will be in the 114 <link xlink:href="#cansas1d_documentation-element-SASroot" 115 ><literal>SASroot</literal></link> 116 <indexterm><primary>SASroot</primary></indexterm> 117 database. This is similar to the root element of a NeXus file (<literal>NXroot</literal>). 110 118 </para></glossdef> 111 119 </glossentry> … … 119 127 <glossterm><code>/cs:SASroot/cs:SASentry</code></glossterm> 120 128 <glossdef><para> 121 [1..inf] A single SAS scan is reported in a SASentry. A SASentry can use the optional "name" attribute to provide a string for this SASentry. Use of this string is not defined by this standard. 129 [1..inf] A single SAS scan is reported in a 130 <link xlink:href="#cansas1d_documentation-element-SASentry" 131 ><literal>SASentry</literal></link>. 132 <indexterm><primary>SASentry</primary></indexterm> 133 This is similar to <literal>NXentry</literal> used by NeXus. 134 A <literal>SASentry</literal> can use an optional <literal>name</literal> attribute to provide a string for this SASentry. 122 135 </para></glossdef> 123 136 </glossentry> … … 125 138 <glossterm><code>/cs:SASroot/cs:SASentry/@name</code></glossterm> 126 139 <glossdef><para> 127 [0..1] Optional string attribute to identify this particular SASentry.140 [0..1] Optional string attribute to identify this particular <literal>SASentry</literal>. Use of the string associated with the <literal>name</literal> attribute is not defined by this standard. 128 141 </para></glossdef> 129 142 </glossentry> -
1dwg/trunk/doc/src/cansas1d_element_SASdata.xml
r128 r129 17 17 <itemizedlist mark="opencircle"> 18 18 <listitem> 19 <indexterm ><primary>SASdata</primary></indexterm>19 <indexterm significance="preferred"><primary>SASdata</primary></indexterm> 20 20 <para> parent: <link xlink:href="#cansas1d_documentation-element-SASentry" 21 21 ><literal>SASentry</literal></link> … … 71 71 <row> 72 72 <entry> 73 < emphasis role="bold">73 <literal> 74 74 Idata 75 75 <indexterm><primary>Idata</primary></indexterm> 76 </ emphasis>76 </literal> 77 77 </entry> 78 78 <entry> container </entry> … … 106 106 <entry> 107 107 <para> 108 < emphasis role="bold">Q</emphasis>108 <literal>Q</literal> 109 109 </para> 110 110 </entry> … … 113 113 <entry> 114 114 <para> 115 <emphasis>Q=(4 pi; / lambda;) sin(theta;)</emphasis> where 116 <emphasis>lambda;</emphasis> is the wavelength of the radiation 117 and <emphasis>2theta;</emphasis> is the angle through which the 115 <inlineequation> 116 <mathphrase><alt>$Q=(4 \pi / \lambda) \sin(\theta)$</alt></mathphrase> 117 </inlineequation> 118 where 119 <inlineequation> 120 <mathphrase><alt>$\lambda$</alt></mathphrase> 121 </inlineequation> 122 is the wavelength of the radiation and 123 <inlineequation> 124 <mathphrase><alt>$2\theta$</alt></mathphrase> 125 </inlineequation> 126 is the angle through which the 118 127 detected radiation has been scattered. The <emphasis role="bold" 119 128 >unit</emphasis> attribute is required. See <link 120 129 xlink:href="#cansas1d_documentation-rules">rules for 121 130 units</link> 122 <!--cansas1d_documentation#Rules -->for acceptable values. Either131 for acceptable values. Either 123 132 <emphasis>1/A</emphasis> or <emphasis>1/nm</emphasis> are 124 133 typical. </para> … … 132 141 <entry> 133 142 <para> 134 < emphasis role="bold">I</emphasis>143 <literal>I</literal> 135 144 </para> 136 145 </entry> … … 160 169 <entry> 161 170 <para> 162 < emphasis role="bold"><emphasis>Idev</emphasis></emphasis>171 <literal>Idev</literal> 163 172 </para> 164 173 </entry> … … 179 188 <entry> 180 189 <para> 181 < emphasis role="bold"><emphasis>Qdev</emphasis></emphasis>190 <literal>Qdev</literal> 182 191 </para> 183 192 </entry> … … 198 207 <entry> 199 208 <para> 200 < emphasis role="bold"><emphasis>dQw</emphasis></emphasis>209 <literal>dQw</literal> 201 210 </para> 202 211 </entry> … … 225 234 <entry> 226 235 <para> 227 < emphasis role="bold"><emphasis>dQl</emphasis></emphasis>236 <literal>dQl</literal> 228 237 </para> 229 238 </entry> … … 252 261 <entry> 253 262 <para> 254 < emphasis role="bold"><emphasis>Qmean</emphasis></emphasis>263 <literal>Qmean</literal> 255 264 </para> 256 265 </entry> … … 272 281 <entry> 273 282 <para> 274 < emphasis role="bold"><emphasis>Shadowfactor</emphasis></emphasis>283 <literal>Shadowfactor</literal> 275 284 </para> 276 285 </entry> … … 289 298 </row> 290 299 <row> 291 <entry><emphasis role="bold"><emphasis role="italic"> {any} 292 </emphasis></emphasis></entry> 300 <entry><literal>{any}</literal></entry> 293 301 <entry> container </entry> 294 302 <entry> [0..inf] </entry> … … 297 305 xlink:href="#cansas1d_documentation-element-any"><emphasis 298 306 role="bold">{any}</emphasis></link> 299 <!--''{any}'' -->for more details. </entry>307 for more details. </entry> 300 308 <entry> 301 309 <para> -
1dwg/trunk/doc/src/elements.xml
r127 r129 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>There are various elements (tag names) in the canSAS1d/1.0 standard. Each of these is 16 described below.</para> 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. 17 There are various elements (tag names) in the canSAS1d/1.0 standard. 18 Each of these is described below. 19 </para> 20 <para> The <emphasis role="italic">Name</emphasis> is the XML tag to be used for this element of the standard. 21 </para> 17 22 <para> The <emphasis role="italic">Type</emphasis> may be a 18 23 <emphasis role="italic">container</emphasis>, -
1dwg/trunk/doc/src/manual.xml
r128 r129 47 47 </revhistory> 48 48 </info> 49 <preface>50 <title>Preface</title>51 <para>52 <mediaobject>53 <imageobject>54 <imagedata fileref="../../graphics/cswikilogo.png" scale="200"/>55 </imageobject>56 </mediaobject>57 CanSAS 1-D Data Format, v1.058 </para>59 <note><para>60 Provide a note here describing CanSAS and the initiative to establish61 a standard file format.62 </para></note>63 <para>64 "CanSAS" stands for "Collective Action for Nomadic Small-Angle Scatterers.65 </para>66 <para>67 This work is the initiative of the CanSAS 1D Data Formats Working Group,68 established at the canSAS-V workshop, NIST, Gaithersburg, Maryland,69 USA from October 29th to 31st 2007. It derives many of its foundations70 from previous works such as the SASXML format, a joint collaboration71 between ISIS and ILL.72 </para>73 <para>74 The home page of the CanSAS 1D Data Formats Working Group75 <link76 xlink:href="http://www.smallangles.net/wgwiki/index.php/1D_Data_Formats_Working_Group"77 >http://www.smallangles.net/wgwiki/index.php/1D_Data_Formats_Working_Group</link>78 describes the members, timelines, and current status.79 There is a discussion page for some matters that preceded this revision.80 <link81 xlink:href="http://www.smallangles.net/wgwiki/index.php/Talk:1D_Data_Formats_Working_Group"82 >http://www.smallangles.net/wgwiki/index.php/Talk:1D_Data_Formats_Working_Group</link> </para>83 </preface>84 49 85 50 <!-- … … 88 53 --> 89 54 55 <xi:include href="preface.xml"/> 90 56 <xi:include href="wiki.xml"/> 57 <xi:include href="specification.xml"/> 58 <xi:include href="tutorial.xml"/> 91 59 <xi:include href="elements.xml"/> 92 60 <xi:include href="bindings.xml"/> 93 61 <xi:include href="casestudies.xml"/> 94 62 <xi:include href="other.xml"/> 63 <!--<xi:include href="appendices.xml"/>--> 95 64 <index/> 96 65 </book> -
1dwg/trunk/doc/src/wiki.xml
r128 r129 14 14 <title>Wiki Manual</title> 15 15 <!-- from: http://www.smallangles.net/wgwiki/index.php/cansas1d_documentation --> 16 <section xml:id="cansas1d_documentation-Disclaimer">17 <title>Disclaimer</title>18 <para>This description is meant to inform the community how to layout the information within19 the XML files. However, should the information in this document and the <link20 xlink:href="http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/cansas1d.xsd"21 >cansas1d/1.0 SAS XML Schema</link>22 (http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/cansas1d.xsd) differ, the XML23 Schema will be deemed to have the most correct description of the standard.</para>24 </section>25 16 <section xml:id="cansas1d_documentation-Objective"> 26 17 <title>Objective</title> 27 <para>One of the first aims of the canSAS (Collective Action for Nomadic Small-Angle 28 Scatterers) forum of users, software developers, and facility staff was to discuss 18 <para>One of the first aims of the canSAS 19 <indexterm><primary>canSAS</primary></indexterm> 20 (Collective Action for Nomadic Small-Angle Scatterers) 21 forum of users, software developers, and facility staff was to discuss 29 22 better sharing of SAS data analysis software. <link 30 23 xlink:href="http://www.smallangles.net/canSAS">CanSAS</link> 31 (http://www.smallangles.net/canSAS) identified that a significant need within the SAS 24 <footnote><para>http://www.smallangles.net/canSAS</para></footnote> 25 identified that a significant need within the SAS 32 26 community can be satisfied by a robust, self-describing, text-based, standard format to 33 27 communicate reduced one-dimensional small-angle scattering data, ''I(Q)'', between users … … 38 32 data of ''I(Q)'' and also any other descriptive information (metadata) about the sample, 39 33 measurement, instrument, processing, or analysis steps. </para> 40 <para>The cansas1d/1.0 standard meets the objectives for a 1D standard, incorporating 34 <para>The cansas1d/1.0 35 <indexterm><primary>cansas1d/1.0 standard</primary></indexterm> 36 standard meets the objectives for a 1D standard, incorporating 41 37 metadata about the measurement, parameters and results of processing or analysis steps. 42 38 Even multiple measurements (related or unrelated) may be included within a single XML … … 58 54 <title>Overview</title> 59 55 <para>The basic elements of the cansas1d/1.0 standard are shown in the following table. 60 After an XML header, the root element of the file is [[cansas1d_SASroot | SASroot]] 61 which contains one or more [[cansas1d_SASentry | SASentry]] elements, each of which 56 After an XML header, the root element of the file is 57 <link xlink:href="#cansas1d_documentation-element-SASroot" 58 ><code>SASroot</code></link> 59 <indexterm><primary>SASroot</primary></indexterm> 60 which contains one or more 61 <link xlink:href="#cansas1d_documentation-element-SASentry" 62 ><code>SASentry</code></link> 63 <indexterm><primary>SASentry</primary></indexterm> 64 elements, each of which 62 65 describes a single experiment (data set, time-slice, step in a series, new sample, 63 etc.). Details of the [[cansas1d_SASentry | SASentry]]element are also shown in the64 next figure. Refer to the [[cansas1d_block_diagrams | block diagrams]] for65 alternative depictions. See <link66 etc.). Details of the <literal>SASentry</literal> element are also shown in the 67 next figure. <!--Refer to the [[cansas1d_block_diagrams | block diagrams]] for 68 alternative depictions.--> See <link 66 69 xlink:href="http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/cansas1d.xml" 67 >http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/cansas1d.xml</link> 70 >cansas1d.xml</link> 71 <footnote> 72 <para> 73 http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/cansas1d.xml 74 </para> 75 </footnote> 68 76 for an example XML file. Examples, Case Studies, and other background information 69 77 are below. More discussion can be found on the 70 [[1D_Data_Formats_Working_Group|canSAS 1D Data Formats Working Group]] page and its 71 [[Talk:1D_Data_Formats_Working_Group|discussion]] page. Details about each specific 72 field (XPath string, XML elements and attributes) are described on the 73 [[cansas1d_definition_of_terms]] page. </para> 78 <link 79 xlink:href="http://www.smallangles.net/wgwiki/index.php/1D_Data_Formats_Working_Group" 80 >canSAS 1D Data Formats Working Group</link> 81 <footnote> 82 <para> 83 http://www.smallangles.net/wgwiki/index.php/1D_Data_Formats_Working_Group 84 </para> 85 </footnote> 86 page and its 87 <link 88 xlink:href="http://www.smallangles.net/wgwiki/index.php/Talk:1D_Data_Formats_Working_Group" 89 >discussion</link> 90 <footnote> 91 <para> 92 http://www.smallangles.net/wgwiki/index.php/Talk:1D_Data_Formats_Working_Group 93 </para> 94 </footnote> 95 page. A 96 <link 97 xlink:href="#cansas1d_documentation-Documentation-Definitions" 98 >glossary</link> 99 <indexterm><primary>glossary</primary><see>definition of terms</see></indexterm> 100 defining the details about each specific field (XPath string, XML elements and attributes) is provided. 101 </para> 74 102 <figure> 75 103 <title>block diagram of minimum elements required for cansas1d/1.0 standard</title> … … 82 110 <itemizedlist> 83 111 <listitem> 84 <para> SASroot: the root element of the file (after the XML header) </para> 85 </listitem> 86 <listitem> 87 <para> SASentry: describes a single experiment (data set, time-slice, step in a 88 series, new sample, etc.) </para> 112 <para> 113 <link xlink:href="#cansas1d_documentation-element-SASroot" 114 ><literal>SASroot</literal></link>: 115 the root element of the file (after the XML header) 116 </para> 117 </listitem> 118 <listitem> 119 <para> 120 <link xlink:href="#cansas1d_documentation-element-SASentry" 121 ><literal>SASentry</literal></link>: 122 describes a single experiment (data set, time-slice, step in a 123 series, new sample, etc.) 124 </para> 89 125 </listitem> 90 126 <listitem> … … 128 164 <entry> 129 165 <emphasis role="bold"> 130 <code>SASroot</code> 166 <link xlink:href="#cansas1d_documentation-element-SASroot" 167 ><code>SASroot</code></link> 131 168 </emphasis> 132 169 </entry> … … 136 173 <entry> 137 174 <emphasis role="bold"> 138 <code> SASentry</code> 175 <link xlink:href="#cansas1d_documentation-element-SASentry" 176 ><code> SASentry</code></link> 139 177 </emphasis> 140 178 </entry> … … 148 186 </emphasis> 149 187 </entry> 150 <entry>for this particular SASentry</entry>188 <entry>for this particular <literal>SASentry</literal></entry> 151 189 </row> 152 190 <row> … … 438 476 <para>The translation and orientation geometry definitions used here are different than 439 477 those used by <link xlink:href="http://www.nanotech.wisc.edu/shadow"><emphasis 440 role="bold">SHADOW</emphasis></link> (http://www.nanotech.wisc.edu/shadow) 478 role="bold">SHADOW</emphasis></link> 479 <footnote><para>http://www.nanotech.wisc.edu/shadow</para></footnote> 441 480 where the <emphasis role="italic">y</emphasis> and <emphasis role="italic" 442 481 >z</emphasis> axes are swapped and the direction of <emphasis role="italic" … … 448 487 <section xml:id="cansas1d_documentation-converting_into_XML"> 449 488 <title>Converting data into the XML format</title> 450 <para>A WWW form ([http://www.smallangles.net/canSAS/xmlWriter/ canSAS/xmlWriter]) is 451 available to translate three-column ASCII text data into the canSAS1d/1.0 XML 489 <para>The 490 <link xlink:href="http://www.smallangles.net/canSAS/xmlWriter/" 491 ><emphasis role="italic"></emphasis>canSAS/xmlWriter</link> 492 <footnote> 493 <para> 494 http://www.smallangles.net/canSAS/xmlWriter/ 495 </para> 496 </footnote> 497 is a WWW form 498 to translate three-column ASCII text data into the canSAS1d/1.0 XML 452 499 format. This form will help you in creating an XML file with all the required 453 500 elements in the correct places. The form requests the SAS data of Q, I, and Idev 454 501 (defined elsewhere on this page) and some basic metadata (title, run, sample info, 455 ...). Press the <nowiki>Submit</nowiki> button and you will receive a nicely502 ...). Press the <code><nowiki>Submit</nowiki></code> button and you will receive a nicely 456 503 formatted WWW page with the SAS data. If you then choose "View page source" (from 457 504 one of your browser menus), you will see the raw XML of the canSAS1d/1.0 XML format … … 643 690 cansas1d/1.0 format. Please refer to the references (and others) [[#Help_for_XML | 644 691 below]] for deeper discussions on foreign elements. </para> 645 <para> The se is one example that demonstrates the use of a foreign namespace: <link692 <para> There is one example that demonstrates the use of a foreign namespace: <link 646 693 xlink:href="http://svn.smallangles.net/trac/canSAS/browser/1dwg/data/Glassy%20Carbon/ISIS/GLASSYC_C4G8G9_withTL.xml" 647 694 >http://svn.smallangles.net/trac/canSAS/browser/1dwg/data/Glassy%20Carbon/ISIS/GLASSYC_C4G8G9_withTL.xml</link>
Note: See TracChangeset
for help on using the changeset viewer.