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Posted to commits@uima.apache.org by sc...@apache.org on 2010/05/06 16:06:04 UTC
svn commit: r941744 [3/7] - in
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--- uima/uimaj/branches/mavenAlign/uima-docbook-tutorials-and-users-guides/src/docbook/tug.aas.xml (added)
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@@ -0,0 +1,283 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE chapter PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
+"http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd"[
+<!ENTITY % uimaents SYSTEM "../../target/docbook-shared/entities.ent" >
+%uimaents;
+]>
+<!--
+Licensed to the Apache Software Foundation (ASF) under one
+or more contributor license agreements. See the NOTICE file
+distributed with this work for additional information
+regarding copyright ownership. The ASF licenses this file
+to you under the Apache License, Version 2.0 (the
+"License"); you may not use this file except in compliance
+with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing,
+software distributed under the License is distributed on an
+"AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+KIND, either express or implied. See the License for the
+specific language governing permissions and limitations
+under the License.
+-->
+<chapter id="ugr.tug.aas">
+ <title>Annotations, Artifacts, and Sofas</title>
+ <titleabbrev>Annotations, Artifacts & Sofas</titleabbrev>
+
+ <para>Up to this point, the documentation has focused on analyzing strings of Unicode text,
+ producing subtypes of Annotations which reference offsets in those strings. This
+ chapter generalizes this concept and shows how other kinds of artifacts can be handled,
+ including non-text things like audio and images, and how you can define your own kinds of
+ <quote>annotations</quote> for these.</para>
+
+ <section id="ugr.tug.aas.terminology">
+ <title>Terminology</title>
+
+ <section id="ugr.tug.aas.artifact">
+ <title>Artifact</title>
+
+ <para>The Artifact is the unstructured thing being analyzed by an annotator. It could
+ be an HTML web page, an image, a video stream, a recorded audio conversation, an MPEG-4
+ stream, etc. Artifacts are often restructured in the course of processing to
+ facilitate particular kinds of analysis. For instance, an HTML page may be converted
+ into a <quote>de-tagged</quote> version. Annotators at different places in the
+ pipeline may be analyzing different versions of the artifact.</para>
+
+ </section>
+
+ <section id="ugr.tug.aas.sofa">
+ <title>Subject of Analysis — Sofa</title>
+
+ <para>Each representation of an Artifact is called a Subject of Analysis, abbreviated
+ using the acronym <quote>Sofa</quote> which stands for <emphasis
+ role="underline">S</emphasis>ubject <emphasis role="underline">
+ OF</emphasis> <emphasis role="underline">A</emphasis>nalysis. Annotation
+ metadata, which have explicit designations of sub-regions of the artifact to which
+ they apply, are always associated with a particular Sofa. For instance, an
+ annotation over text specifies two features, the begin and end, which represent the
+ character offsets into the text string Sofa being analyzed.</para>
+
+ <para>Other examples of representations of Artifacts, which could be Sofas include:
+ An HTML web page, a detagged web page, the translated text of that document, an audio or
+ video stream, closed-caption text from a video stream, etc.</para>
+
+ <para>Often, there is one Sofa being analyzed in a CAS. The next chapter will show how
+ UIMA facilitates working with multiple representations of an artifact at the same
+ time, in the same CAS.</para>
+
+ </section>
+ </section>
+
+ <section id="ugr.tug.aas.sofa_data_formats">
+ <title>Formats of Sofa Data</title>
+
+ <para>Sofa data can be Java Unicode Strings, Feature Structure arrays of primitive
+ types, or a URI which references remote data available via a network
+ connection.</para>
+
+ <para>The arrays of primitive types can be things like byte arrays or float arrays, and are
+ intended to be used for artifacts like audio data, image data, etc.</para>
+
+ <para>The URI form holds a URI specification String.</para>
+
+ <note><para>Sofa data can be "serialized" using an XML format; when it is, the String data
+ being serialized must not include invalid XML characters. See
+ <xref linkend="ugr.tug.xmi_emf.xml_character_issues"/>.
+ </para></note>
+
+ </section>
+
+ <section id="ugr.tug.aas.setting_accessing_sofa_data">
+ <title>Setting and Accessing Sofa Data</title>
+
+ <section id="ugr.tug.aas.setting_sofa_data">
+ <title>Setting Sofa Data</title>
+
+ <para>When a CAS is created, you can set its Sofa Data, just one time; this property
+ insures that metadata describing regions of the Sofa remain valid. As a consequence,
+ the following methods that set data for a given Sofa can only be called once for a given
+ Sofa.</para>
+
+ <para>The following methods on the CAS set the Sofa Data to one of the 3 formats. Assume
+ that the variable <quote>aCas</quote> holds a reference to a CAS:</para>
+
+
+ <programlisting><?db-font-size 80% ?>aCas.<emphasis role="bold">setSofaDataString</emphasis>(document_text_string, mime_type_string);
+aCas.<emphasis role="bold">setSofaDataArray</emphasis>(feature_structure_primitive_array, mime_type_string);
+aCas.<emphasis role="bold">setSofaDataURI</emphasis>(uri_string, mime_type_string);</programlisting>
+
+ <para>In addition, the method
+ <literal>aCas.setDocumentText(document_text_string)</literal> may still be
+ used, and is equivalent to <literal>setSofaDataString(string,
+ "text")</literal>. The mime type is currently not used by the UIMA framework, but may
+ be set and retrieved by user code.</para>
+
+ <para>Feature Structure primitive arrays are all the UIMA Array types except arrays of
+ Feature Structures, Strings, and Booleans. Typically, these are arrays of bytes,
+ but can be other types, such as floats, longs, etc.</para>
+
+ <para>The URI string should conform to the standard URI format.</para>
+
+ </section>
+
+ <section id="ugr.tug.aas.accessing_sofa_data">
+ <title>Accessing Sofa Data</title>
+
+ <para>The analysis algorithms typically work with the Sofa data. The following
+ methods on the CAS access the Sofa Data:</para>
+
+
+ <programlisting>String aCas.getDocumentText();
+String aCas.getSofaDataString();
+FeatureStructure aCas.getSofaDataArray();
+String aCas.getSofaDataURI();
+String aCas.getSofaMimeType();</programlisting>
+
+ <para>The <literal>getDocumentText</literal> and
+ <literal>getSofaDataString</literal> return the same text string. The
+ <literal>getSofaDataURI</literal> returns the URI itself, not the data the URI is
+ pointing to. You can use standard Java I/O capabilities to get the data associated
+ with the URI, or use the UIMA Framework Streaming method described next.</para>
+
+ </section>
+
+ <section id="ugr.tug.aas.accessing_sofa_data_using_java_stream">
+ <title>Accessing Sofa Data using a Java Stream</title>
+
+ <para>The framework provides a consistent method for accessing the Sofa data,
+ independent of it being stored locally, or accessed remotely using the URI. Get a Java
+ InputStream instance from the Sofa data using:</para>
+
+
+ <programlisting>InputStream inputStream = aCas.getSofaDataStream();</programlisting>
+
+ <itemizedlist spacing="compact"><listitem><para>If the data is local, this method
+ returns a ByteArrayInputStream. This stream provides bytes.
+
+ <itemizedlist><listitem><para>If the Sofa data was set using setDocumentText or
+ setSofaDataString, the String is converted to bytes by using the UTF-8
+ encoding.</para></listitem>
+
+ <listitem><para>If the Sofa data was set as a DataArray, the bytes in the data array
+ are serialized, high-byte first. </para></listitem></itemizedlist>
+ </para></listitem>
+
+ <listitem><para>If the Sofa data was specified as a URI, this method returns the
+ handle from url.openStream(). Java offers built-in support for several URI
+ schemes including <quote>FILE:</quote>, <quote>HTTP:</quote>,
+ <quote>FTP:</quote> and has an extensible mechanism,
+ <literal>URLStreamHandlerFactory</literal>, for customizing access to an
+ arbitrary URI. See more details at <ulink
+ url="http://java.sun.com/j2se/1.5.0/docs/api/java/net/URLStreamHandlerFactory.html"/>
+ . </para></listitem></itemizedlist>
+
+ </section>
+ </section>
+
+ <section id="ugr.tug.aas.sofa_fs">
+ <title>The Sofa Feature Structure</title>
+
+ <para>Information about a Sofa is contained in a special built-in Feature Structure of
+ type <literal>uima.cas.Sofa</literal>. This feature structure is created and
+ managed by the UIMA Framework; users must not create it directly. Although these Sofa
+ type instances are implemented as standard feature structures, <emphasis>generic
+ CAS APIs can not be used to create Sofas or set their features</emphasis>. Instead,
+ Sofas are created implicitly by the creation of new CAS views. Similarly, Sofa features
+ are set by CAS methods such as <literal>cas.setDocumentText()</literal>.</para>
+
+ <para>Features of the Sofa type include</para>
+
+ <itemizedlist><listitem><para>SofaID: Every Sofa in a CAS has a unique SofaID. SofaIDs
+ are the primary handle for access. This ID is often the same as the name string given to the
+ Sofa by the developer, but it can be mapped to a different name (see <olink
+ targetdoc="&uima_docs_tutorial_guides;"
+ targetptr="ugr.tug.mvs.sofa_name_mapping"/>.</para></listitem>
+
+ <listitem><para>Mime type: This string feature can be used to describe the type of the
+ data represented by a Sofa. It is not used by the framework; the framework provides
+ APIs to set and get its value.</para></listitem>
+
+ <listitem><para>Sofa Data: The Sofa data itself. This data can be resident in the CAS or
+ it can be a reference to data outside the CAS. </para></listitem></itemizedlist>
+
+ </section>
+
+ <section id="ugr.tug.aas.annotations">
+ <title>Annotations</title>
+
+ <para>Annotators add meta data about a Sofa to the CAS. It is often useful to have this
+ metadata denote a region of the Sofa to which it applies. For instance, assuming the Sofa
+ is a String, the metadata might describe a particular substring as the name of a person.
+ The built-in UIMA type, uima.tcas.Annotation, has two extra features that enable this
+ - the begin and end features - which denote a character position offset into the text
+ string being analyzed.</para>
+
+ <para>The concept of <quote>annotations</quote> can be generalized for non-string
+ kinds of Sofas. For instance, an audio stream might have an audio annotation which
+ describes sounds regions in terms of floating point time offsets in the Sofa. An image
+ annotation might use two pairs of x,y coordinates to define the region the annotation
+ applies to.</para>
+
+ <section id="ugr.tug.aas.built_in_annotation_types">
+ <title>Built-in Annotation types</title>
+
+ <para>The built-in CAS type, <literal>uima.tcas.Annotation</literal>, is just one
+ kind of definition of an Annotation. It was designed for annotating text strings, and
+ has begin and end features which describe which substring of the Sofa being
+ annotated.</para>
+
+ <para>For applications which have other kinds of Sofas, the UIMA developer will design
+ their own kinds of Annotation types, as needed to describe an annotation, by
+ declaring new types which are subtypes of
+ <literal>uima.cas.AnnotationBase</literal>. For instance, for images, you
+ might have the concept of a rectangular region to which the annotation applies. In
+ this case, you might describe the region with 2 pairs of x, y coordinates.</para>
+
+ </section>
+
+ <section id="ugr.tug.aas.annotations_associated_sofa">
+ <title>Annotations have an associated Sofa</title>
+
+ <para>Annotations are always associated with a particular Sofa. In subsequent
+ chapters, you will learn how there can be multiple Sofas associated with an artifact;
+ which Sofa an annotation refers to is described by the Annotation feature structure
+ itself.</para>
+
+ <para>All annotation types extend from the built-in type uima.cas.AnnotationBase.
+ This type has one feature, a reference to the Sofa associated with the annotation.
+ This value is currently used by the Framework to support the getCoveredText() method
+ on the annotation instance - this returns the portion of a text Sofa that the
+ annotation spans. It also is used to insure that the Annotation is indexed only in the
+ CAS View associated with this Sofa.</para>
+ </section>
+ </section>
+
+ <section id="ugr.tug.aas.annotationbase">
+ <title>AnnotationBase</title>
+
+ <para>A built-in type, <literal>uima.cas.AnnotationBase</literal>, is provided by
+ UIMA to allow users to extend the Annotation capabilities to different kinds of
+ Annotations. The <literal>AnnotationBase</literal> type has one feature, named
+ <literal>sofa</literal>, which holds a reference to the
+ <literal>Sofa</literal> feature structure with which this annotation is associated.
+ The <literal>sofa</literal> feature is automatically set when creating an annotation
+ (meaning — any type derived from the built-in
+ <literal>uima.cas.AnnotationBase</literal> type); it should not be set by the user.</para>
+
+ <para>There is one method, <literal>getView</literal>(), provided by
+ <literal>AnnotationBase</literal> that returns the CAS View for the Sofa the
+ annotation is pointing at. Note that this method always returns a CAS, even when applied
+ to JCas annotation instances.</para>
+
+ <para>The built-in type <literal>uima.tcas.Annotation</literal> extends
+ <literal>uima.cas.AnnotationBase</literal> and adds two features, a begin and an
+ end feature, which are suitable for identifying a span in a text string that the
+ annotation applies to. Users may define other extensions to
+ <literal>AnnotationBase</literal> with alternative specifications that can
+ denote a particular region within the subject of analysis, as appropriate to their
+ application.</para>
+
+ </section>
+</chapter>
\ No newline at end of file