Changeset 129


Ignore:
Timestamp:
Oct 2, 2009 5:47:47 PM (10 years ago)
Author:
prjemian
Message:

more cross-references, formatting, & indices, refs #19

Location:
1dwg/trunk/doc
Files:
3 added
7 edited

Legend:

Unmodified
Added
Removed
  • 1dwg/trunk/doc/src/cansas1d_binding_Python.xml

    r127 r129  
    3939    <section><title>gnosis.xml.objectify</title> 
    4040        <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>). 
    4247        </para> 
    4348        <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) 
    4553        </para> 
    4654        <para> 
     
    4957        <section><title>installation</title> 
    5058            <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 ... 
    5263                <programlisting>cd /tmp 
    5364wget 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  
    2121        $Date$ 
    2222    </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> 
    2626    <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>  
    2832    </para> 
    2933    <itemizedlist mark="opencircle"><listitem> 
     
    107111                <glossterm><code>/cs:SASroot</code></glossterm> 
    108112                <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>). 
    110118                </para></glossdef> 
    111119            </glossentry> 
     
    119127                <glossterm><code>/cs:SASroot/cs:SASentry</code></glossterm> 
    120128                <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.  
    122135                </para></glossdef> 
    123136            </glossentry> 
     
    125138                <glossterm><code>/cs:SASroot/cs:SASentry/@name</code></glossterm> 
    126139                <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. 
    128141                </para></glossdef> 
    129142            </glossentry> 
  • 1dwg/trunk/doc/src/cansas1d_element_SASdata.xml

    r128 r129  
    1717    <itemizedlist mark="opencircle"> 
    1818        <listitem> 
    19             <indexterm><primary>SASdata</primary></indexterm> 
     19            <indexterm significance="preferred"><primary>SASdata</primary></indexterm> 
    2020            <para> parent: <link xlink:href="#cansas1d_documentation-element-SASentry" 
    2121                ><literal>SASentry</literal></link> 
     
    7171                    <row> 
    7272                        <entry> 
    73                             <emphasis role="bold"> 
     73                            <literal> 
    7474                                Idata 
    7575                                <indexterm><primary>Idata</primary></indexterm> 
    76                             </emphasis> 
     76                            </literal> 
    7777                        </entry> 
    7878                        <entry> container </entry> 
     
    106106                        <entry> 
    107107                            <para> 
    108                                 <emphasis role="bold">Q</emphasis> 
     108                                <literal>Q</literal> 
    109109                            </para> 
    110110                        </entry> 
     
    113113                        <entry> 
    114114                            <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 
    118127                                detected radiation has been scattered. The <emphasis role="bold" 
    119128                                    >unit</emphasis> attribute is required. See <link 
    120129                                    xlink:href="#cansas1d_documentation-rules">rules for 
    121130                                    units</link> 
    122                                 <!--cansas1d_documentation#Rules --> for acceptable values. Either 
     131                                for acceptable values. Either 
    123132                                    <emphasis>1/A</emphasis> or <emphasis>1/nm</emphasis> are 
    124133                                typical. </para> 
     
    132141                        <entry> 
    133142                            <para> 
    134                                 <emphasis role="bold">I</emphasis> 
     143                                <literal>I</literal> 
    135144                            </para> 
    136145                        </entry> 
     
    160169                        <entry> 
    161170                            <para> 
    162                                 <emphasis role="bold"><emphasis>Idev</emphasis></emphasis> 
     171                                <literal>Idev</literal> 
    163172                            </para> 
    164173                        </entry> 
     
    179188                        <entry> 
    180189                            <para> 
    181                                 <emphasis role="bold"><emphasis>Qdev</emphasis></emphasis> 
     190                                <literal>Qdev</literal> 
    182191                            </para> 
    183192                        </entry> 
     
    198207                        <entry> 
    199208                            <para> 
    200                                 <emphasis role="bold"><emphasis>dQw</emphasis></emphasis> 
     209                                <literal>dQw</literal> 
    201210                            </para> 
    202211                        </entry> 
     
    225234                        <entry> 
    226235                            <para> 
    227                                 <emphasis role="bold"><emphasis>dQl</emphasis></emphasis> 
     236                                <literal>dQl</literal> 
    228237                            </para> 
    229238                        </entry> 
     
    252261                        <entry> 
    253262                            <para> 
    254                                 <emphasis role="bold"><emphasis>Qmean</emphasis></emphasis> 
     263                                <literal>Qmean</literal> 
    255264                            </para> 
    256265                        </entry> 
     
    272281                        <entry> 
    273282                            <para> 
    274                                 <emphasis role="bold"><emphasis>Shadowfactor</emphasis></emphasis> 
     283                                <literal>Shadowfactor</literal> 
    275284                            </para> 
    276285                        </entry> 
     
    289298                    </row> 
    290299                    <row> 
    291                         <entry><emphasis role="bold"><emphasis role="italic"> {any} 
    292                                 </emphasis></emphasis></entry> 
     300                        <entry><literal>{any}</literal></entry> 
    293301                        <entry> container </entry> 
    294302                        <entry> [0..inf] </entry> 
     
    297305                                xlink:href="#cansas1d_documentation-element-any"><emphasis 
    298306                                    role="bold">{any}</emphasis></link> 
    299                             <!--''{any}'' --> for more details. </entry> 
     307                            for more details. </entry> 
    300308                        <entry> 
    301309                            <para> 
  • 1dwg/trunk/doc/src/elements.xml

    r127 r129  
    1313    xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xi="http://www.w3.org/2001/XInclude"> 
    1414    <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> 
    1722    <para> The <emphasis role="italic">Type</emphasis> may be a  
    1823        <emphasis role="italic">container</emphasis>,  
  • 1dwg/trunk/doc/src/manual.xml

    r128 r129  
    4747        </revhistory> 
    4848    </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, v1.0 
    58         </para> 
    59         <note><para> 
    60             Provide a note here describing CanSAS and the initiative to establish 
    61             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 foundations 
    70             from previous works such as the SASXML format, a joint collaboration 
    71             between ISIS and ILL. 
    72         </para> 
    73         <para> 
    74             The home page of the CanSAS 1D Data Formats Working Group 
    75             <link  
    76                 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             <link  
    81                 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> 
    8449 
    8550        <!-- 
     
    8853        --> 
    8954 
     55        <xi:include href="preface.xml"/> 
    9056    <xi:include href="wiki.xml"/> 
     57    <xi:include href="specification.xml"/> 
     58    <xi:include href="tutorial.xml"/> 
    9159    <xi:include href="elements.xml"/> 
    9260    <xi:include href="bindings.xml"/> 
    9361    <xi:include href="casestudies.xml"/> 
    9462    <xi:include href="other.xml"/> 
     63        <!--<xi:include href="appendices.xml"/>--> 
    9564    <index/> 
    9665</book> 
  • 1dwg/trunk/doc/src/wiki.xml

    r128 r129  
    1414    <title>Wiki Manual</title> 
    1515    <!-- 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 within 
    19             the XML files. However, should the information in this document and the <link 
    20                 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 XML 
    23             Schema will be deemed to have the most correct description of the standard.</para> 
    24     </section> 
    2516    <section xml:id="cansas1d_documentation-Objective"> 
    2617        <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 
    2922            better sharing of SAS data analysis software. <link 
    3023                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 
    3226            community can be satisfied by a robust, self-describing, text-based, standard format to 
    3327            communicate reduced one-dimensional small-angle scattering data, ''I(Q)'', between users 
     
    3832            data of ''I(Q)'' and also any other descriptive information (metadata) about the sample, 
    3933            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 
    4137            metadata about the measurement, parameters and results of processing or analysis steps. 
    4238            Even multiple measurements (related or unrelated) may be included within a single XML 
     
    5854            <title>Overview</title> 
    5955            <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 
    6265                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 the 
    64                 next figure. Refer to the [[cansas1d_block_diagrams | block diagrams]] for 
    65                 alternative depictions. See <link 
     66                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 
    6669                    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> 
    6876                for an example XML file. Examples, Case Studies, and other background information 
    6977                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> 
    74102            <figure> 
    75103                <title>block diagram of minimum elements required for cansas1d/1.0 standard</title> 
     
    82110            <itemizedlist> 
    83111                <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> 
    89125                </listitem> 
    90126                <listitem> 
     
    128164                                    <entry> 
    129165                                        <emphasis role="bold"> 
    130                                             <code>SASroot</code> 
     166                                            <link xlink:href="#cansas1d_documentation-element-SASroot" 
     167                                                ><code>SASroot</code></link> 
    131168                                        </emphasis> 
    132169                                    </entry> 
     
    136173                                    <entry> 
    137174                                        <emphasis role="bold"> 
    138                                             <code>&#160;SASentry</code> 
     175                                            <link xlink:href="#cansas1d_documentation-element-SASentry" 
     176                                                ><code>&#160;SASentry</code></link> 
    139177                                        </emphasis> 
    140178                                    </entry> 
     
    148186                                        </emphasis> 
    149187                                    </entry> 
    150                                     <entry>for this particular SASentry</entry> 
     188                                    <entry>for this particular <literal>SASentry</literal></entry> 
    151189                                </row> 
    152190                                <row> 
     
    438476            <para>The translation and orientation geometry definitions used here are different than 
    439477                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> 
    441480                where the <emphasis role="italic">y</emphasis> and <emphasis role="italic" 
    442481                    >z</emphasis> axes are swapped and the direction of <emphasis role="italic" 
     
    448487        <section xml:id="cansas1d_documentation-converting_into_XML"> 
    449488            <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 
    452499                format. This form will help you in creating an XML file with all the required 
    453500                elements in the correct places. The form requests the SAS data of Q, I, and Idev 
    454501                (defined elsewhere on this page) and some basic metadata (title, run, sample info, 
    455                 ...). Press the &lt;nowiki>Submit&lt;/nowiki> button and you will receive a nicely 
     502                ...). Press the <code>&lt;nowiki>Submit&lt;/nowiki></code> button and you will receive a nicely 
    456503                formatted WWW page with the SAS data. If you then choose "View page source" (from 
    457504                one of your browser menus), you will see the raw XML of the canSAS1d/1.0 XML format 
     
    643690                cansas1d/1.0 format. Please refer to the references (and others) [[#Help_for_XML | 
    644691                below]] for deeper discussions on foreign elements. </para> 
    645             <para> These is one example that demonstrates the use of a foreign namespace: <link 
     692            <para> There is one example that demonstrates the use of a foreign namespace: <link 
    646693                    xlink:href="http://svn.smallangles.net/trac/canSAS/browser/1dwg/data/Glassy%20Carbon/ISIS/GLASSYC_C4G8G9_withTL.xml" 
    647694                    >http://svn.smallangles.net/trac/canSAS/browser/1dwg/data/Glassy%20Carbon/ISIS/GLASSYC_C4G8G9_withTL.xml</link> 
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