Changeset 7640


Ignore:
Timestamp:
Mar 11, 2019, 2:13:29 PM (5 years ago)
Author:
Nicklas Nordborg
Message:

References #2136: Remove support for spot images

Updated documentation.

Location:
trunk/doc/src
Files:
1 deleted
9 edited

Legend:

Unmodified
Added
Removed

  • trunk/doc/src/docbook/admin/installation.xml

    r7631 r7640  
    9393        by the upgrade script. The recommendation is to replace this feature with
    9494        an external files solution instead.
     95      </para>
     96   
     97      <bridgehead>Spot images support has been removed</bridgehead>
     98      <para>
     99        It is no longer possible to create new spot images or view existing
     100        spot images via the BASE web client. Existing source image files and
     101        zip archives with generated spot images have not been removed.
    95102      </para>
    96103     

  • trunk/doc/src/docbook/appendix/coreplugins.xml

    r6049 r7640  
    612612
    613613      <varlistentry>
    614         <term>Spot images creator</term>
    615         <listitem>
    616           <para>
    617             Converts a full-size image into JPEG images for each spot.
    618             No configuration is needed.
    619           </para>
    620         </listitem>
    621       </varlistentry>
    622 
    623       <varlistentry>
    624614        <term>TAR file unpacker</term>
    625615        <listitem>

  • trunk/doc/src/docbook/appendix/incompatible.xml

    r7610 r7640  
    4242    <para>
    4343      API that is related to the secondary storage feature has been removed. For example,
    44       In the <classname docapi="net.sf.basedb.core">File</classname> class, <code>getAction()/setAction()</code>
     44      in the <classname docapi="net.sf.basedb.core">File</classname> class, <code>getAction()/setAction()</code>
    4545      has been removed. In the <classname docapi="net.sf.basedb.core">Location</classname> enumeration,
    4646      <code>SECONDARY</code> has been removed.   
     47    </para>
     48   
     49    <bridgehead id="appendix.incompatible.spotimages">Spot images support has been removed</bridgehead>
     50    <para>
     51      API that is related to creating and viewing spot images has been removed. For example,
     52      in the <classname docapi="net.sf.basedb.core">RawBioAssay</classname> class, the
     53      <code>getSpotImages()</code> method has been removed. The <classname>SpotImages</classname>
     54      class has been removed and there are several other minor changes related to this.
     55      There is no replacement.
    4756    </para>
    4857   

  • trunk/doc/src/docbook/appendix/update_warnings.xml

    r7631 r7640  
    7676      by the upgrade script. The recommendation is to replace this feature with
    7777      an external files solution instead.
     78    </para>
     79   
     80    <bridgehead>Spot images support has been removed</bridgehead>
     81    <para>
     82      It is no longer possible to create new spot images or view existing
     83      spot images via the BASE web client. Existing source image files and
     84      zip archives with generated spot images have not been removed.
    7885    </para>
    7986 

  • trunk/doc/src/docbook/developer/base_api.xml

    r7598 r7640  
    22332233       
    22342234      </sect3>
    2235      
    2236       <sect3 id="data_api.rawdata.spotimages">
    2237         <title>Spot images</title>
    2238        
    2239         <para>
    2240         Spot images can be created if you have the original image
    2241         files. BASE can use 1-3 images as sources for the red, green
    2242         and blue channel respectively. The creation of spotimages requires
    2243         that x and y coordinates are given for each raw data spot. The scaling
    2244         and offset values are used to convert the coordinates to pixel
    2245         coordinates. With this information BASE is able to cut out a square
    2246         from the source images that, theoretically, contains a specific spot and
    2247         nothing else. The spot images are gamma-corrected independently and then
    2248         put together into PNG images that are stored in a zip file.
    2249         </para>
    2250       </sect3>
    2251      
     2235       
    22522236    </sect2>
    22532237

  • trunk/doc/src/docbook/user/project_permission.xml

    r7222 r7640  
    8989              <para>
    9090              Permission to add, update or delete annotations on an item.
    91               In addition to this permission, <term>Use</term> permission
     91              In addition to this permission, <guilabel>Use</guilabel> permission
    9292              is required on the annotation type.
    9393              </para>

  • trunk/doc/src/docbook/user/rawbioassays.xml

    r5800 r7640  
    338338  </sect2>
    339339
    340   <sect2 id="experiments_analysis.spotimages">
    341     <title>Spot images</title>
    342     <para>
    343       This section only applies to microarray platforms where
    344       a coordinate system is used to identify spots on the
    345       array slides. The raw data must contain X and Y
    346       coordinates of each spot.
    347     </para>
    348    
    349     <para>
    350       After raw data has been imported into the database
    351       you will find that a <guibutton>Create spot images&hellip;</guibutton>
    352       button appears in the toolbar on the single-item view
    353       for the raw bioassay. Click on this button to open
    354       a window that allows you to specify parameters for the
    355       spot image extraction.
    356     </para>
    357    
    358     <figure id="experiments_analysis.figures.spotimage">
    359       <title>Create spot images</title>
    360       <screenshot>
    361         <mediaobject>
    362           <imageobject><imagedata
    363             fileref="figures/create_spot_images.png" format="PNG"
    364             /></imageobject>
    365         </mediaobject>
    366       </screenshot>
    367     </figure>
    368    
    369     <helptext external_id="rawbioassay.edit.spotimages"
    370       title="Create spot images">
    371      
    372     <variablelist>
    373       <varlistentry>
    374         <term><guilabel>X/Y scale and offset</guilabel></term>
    375         <listitem>
    376           <para>
    377             For the spot image creation process to be able
    378             to find the spots, the X and Y coordinates from
    379             the raw data must be converted into image pixel
    380             values. The formula used is:
    381             <code>pixelX = (rawX - offsetX) / scaleX</code>
    382           </para>
    383          
    384           <important>
    385             It is important that you get these values correct,
    386             or the spot image creation process may fail or generate
    387             incorrect spot images.
    388           </important>
    389          
    390         </listitem>
    391       </varlistentry>
    392      
    393       <varlistentry>
    394         <term><guilabel>Spot size</guilabel></term>
    395         <listitem>
    396           <para>
    397             The spot size is given in pixels and is the width and
    398             hight around each spot that is large enough to contain
    399             the spot without having too much empty space or
    400             neighbouring spots around it.
    401           </para>
    402      
    403         </listitem>
    404       </varlistentry>
    405      
    406       <varlistentry>
    407         <term><guilabel>Gamma correction</guilabel></term>
    408         <listitem>
    409           <para>
    410             Gamma correction is needed to make the images
    411             look good on computer displays. A value between
    412             1.8 and 2.2 is usually best.
    413             See <ulink url="http://en.wikipedia.org/wiki/Gamma_correction"
    414               >http://en.wikipedia.org/wiki/Gamma_correction</ulink>
    415             for more information.
    416           </para>
    417      
    418         </listitem>
    419       </varlistentry>
    420      
    421       <varlistentry>
    422         <term><guilabel>Quality</guilabel></term>
    423         <listitem>
    424           <para>
    425             The quality setting to use when saving the generated
    426             spot images as JPEG images. A value between 0 = poor
    427             and 1 = good can be used.
    428           </para>
    429         </listitem>
    430       </varlistentry>
    431      
    432       <varlistentry>
    433         <term><guilabel>Red, green and blue image files</guilabel></term>
    434         <listitem>
    435           <para>
    436             You must select which scanned image files to use for the
    437             red, green and blue component of the generated spot images.
    438             Use the <guibutton>Select&hellip;</guibutton> buttons
    439             to select existing images or upload new ones.
    440             The original image files must be 8- or
    441             16-bit grey scale images. Some scanners, for
    442             example Genepix, can create TIFF files with more than
    443             one image in each file. BASE supports this and uses
    444             the images in the order they appear in the TIFF file.
    445           </para>
    446          
    447           <note>
    448             Avoid TIFF images which also contains previews
    449             of the full image. BASE may use the wrong image
    450             with an error as the result. If you have multi-image
    451             TIFF files these must only contain the full images.
    452           </note>
    453          
    454         </listitem>
    455       </varlistentry>
    456       <varlistentry>
    457         <term><guilabel>Save as</guilabel></term>
    458         <listitem>
    459           <para>
    460             Specify the path and filename where the generated spot
    461             images should be saved. The process will create
    462             a single zip file containing all the images.
    463           </para>
    464         </listitem>
    465       </varlistentry>
    466      
    467       <varlistentry>
    468         <term><guilabel>Overwrite existing file</guilabel></term>
    469         <listitem>
    470           <para>
    471             If a file with the same name already exists you
    472             must mark this checkbox to overwrite it.
    473           </para>
    474         </listitem>
    475       </varlistentry>
    476     </variablelist>
    477    
    478     <para>
    479       Click on the <guibutton>Create</guibutton> button
    480       to add the spot image creation job to the job queue,
    481       or on &gbCancel; to abort.
    482     </para>
    483    
    484     </helptext>
    485   </sect2>
    486340</sect1>
    487341   
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