Scientific Image DataBase

File Release Notes and Changelog

Release Name: 0.17

Notes: <h3>Scientific Image DataBase, v0.17 release notes</h3> This release adds more javascript code to check users input in forms. The frame speed of mpeg movies produced by sidb can now be set by the user. Users can set an 'expiration date' for their images, and the database will indeed delete the expired images (after warning by email). Since I moved to the States, the US date format (m-d-y) is now also supported. See the change log for details. To upgrade from previous versions (highly recomended), simply copy all files over the old ones. You can do so by copying the sidbv017.tar.gz archive to the directory containing your sidb directory, i.e. 'ls' should show: sidb &nbsp sidbv017.tar.gz Now issue the following commands while logged in as your system's webdaemon (wwwrun/apache/winnetou, or whatever) gunzip sidbv017.tar.gz tar -xvf sidbv017.tar Login into the database (using your browser), choose globals, and press the 'submit' button. All necessary adjustments will be made by the script install.php. To freshly install sidb, follow these instructions: <h3>You will need the following:</h3> <ul> <li><a href="http://www.apache.org">Apache webserver </a>(tested with version 1.3.12)</li> <li><a href="http://php.net">php (</a>tested with 4.0.0 up to 4.0.4pl1)</li> <li><a href="http://postgresql.org">Postgresql </a>(tested with 7.0)</li> <li><a href="http://www.imagemagick.org">Imagemagick </a>(only convert, tested with 5.2.0).</li> <li>You also will like to use <a href="http://www.mpeg.org/MSSG">mpeg2encode </a> to generate MPEG movies, (see note below) </li> <li>Iptcutil (distributed with the latest version of Imagemagick) is a small utility that can extract usefull information (embedded comments) from image files.</li> <li>To generate thumbnails from 3-D images (Leica, Zeiss, and Biorad confocal images as well as files in ics/ids format) you will also need the batch version of the Huygens software. A freeware version of Huygens running under linux which has all the functionality needed in the database can be downloaded from the <a href="http://www.svi.nl">SVI website</a>. </li> <li><a href="http://http://rsb.info.nih.gov/ij/">Imagej</a> is an image processing and analysis program written in Java by Wayne Rasband. You can send it as an applet to your users, automatically opening an image from the database. An ImageJ version patched for this purpose can be downloaded from <a href="http://sourceforge.net/project/showfiles.php?group_id=17393">http://sourceforge.net/project/showfiles.php?group_id=17393</a></li> </ul> <li>A properly configured sendmail (see your systems documentation) will allow sidb to send email to users whith images whose expiration date is about to expire.</li> Except for Huygens and ImageJ, most needed software is included in the current linux distributions (I tested redhat 7.0 and 7.1 as well as SUSE 7.0 and 7.1, but others should work equilly well). <h4>Installation Instructions</h4> Login as the user running the webserver (wwwrun under SUSE, apache under Red Hat). Navigate to a folder in your web-tree (under SUSE, the highest level directory in your web tree is /usr/local/httpd/htdocs). Unpack the file 'sidav0xxb.tar.gz' by issuing the following commands: gunzip sidbv0xx.tar.gz tar -xvf sidbv0xx.tar All sidb related files are placed in a directory called 'sidb'. You can place sidb in your top-level web-directory, making it possible to start sidb using http://localhost. For this to work, make sure there is no file called index.htm in your top-level web-directory and that 'index.php' is an argument for the apache variable 'DirectoryIndex' in the file 'httpd.conf'. If you did not install the files as the user running the webserver, changes ownership now, for instance by entering (you have to be root for this to work): chown -R wwwrun sidb The following subdirectories are created: 'archive', 'thumbnails', 'includes', 'images', and 'docs'. All image files you upload to sidb will be stored unchanged (but renamed by adding a number in front of the original filename) in the directory 'archive'. For increased security, move 'archive' and 'thumbnails' outof the web-tree, but make sure they can be read and written by the account running your webserver daemon (and preferably nobody else). You may perform this 'move' during the installation procedure (see below). Leave the other directories within the web-tree unchanged. For increased security, you may set your Apache settings such that 'includes' cannot be read directly through a browser (although I think this is only needed for the paranoid among us). Point your browser to the file install.php in the top-level directory. Follow the instructions carefully. Check the following php directives (they are stored in a file called "php.ini" which location you can find by running the script info.php): <table border=0> <tr><td>max_execution_time:</td><td>You might want to increase this to 120 sec.</td></tr> <tr><td>display_errors: </td><td>For a 'production' site, switch this off.</td></tr> <tr><td>register_globals: </td><td>Set to 'Off'. Leaving this on is a potential security hazard.</td</tr> <tr><td>post_max_size: </td><td>Together with 'upload_max_size' these determine the maximum file size that can be uploaded to your server through html file uploads.</td></tr> <tr><td>magick_quotes_gpc: </td><td>Should be 'On'.</td></tr> <tr><td>file_uploads: </td><td>Should be 'On'. </td></tr> <tr><td>upload_max_filesize: </td><td>Together with 'post_max_size' this one determines the maximum file size that can be uploaded to your server through html file uploads.</td></tr> <tr><td>safe_mode: </td><td>Should be 'Off', or 'outside' scripts/programs can not be called. Suse has this 'On' by default. You might want to check this switch if your sidb installation does not create thumbnails..</td></tr> </table> If you so wish, you can patch ImageJ yourself. Move the ij.jar file to be patched to your sidb directory. Issue the commands: cd imagej/classes zip -r ../../ij.jar * Mpeg2encode is installed along with Imagemagick in some distributions, but not in others. If no movies are generated, check whether mpeg2encode is installed on your system (by issuing the command "mpeg2encode"). If not, check your distributions CDs or download the (<a href="ftp://ftp.mpeg.org/pub/mpeg">sources</a> and compile them. 'Vacuum' the database regularly (the 'vacuum' button can be found under 'globals'. At the same time, images whose exiration date have past will be removed (after giving the owners notice by email at least one week in advance). If you have problems, please let <a href=mailto:stuurman@rulbim.leidenuniv.nl >me </a>know Nico Stuurman, last changed: July 17, 20001

Changes: <h3>Change log for the Scientific Image Database</h3> <h4>Version 0.17</h4> <ul> <li>Fixed a bug ignoring values entered in the first installation form when 'register-globals' was switched Off.</li> <li>Added code to send email when an image expires, and delete it a week later. Currently invoked by pressing the 'Vacuum' button.</li> <li>Added 'expiration date' field (as suggested by Erik Manders).</li> <li>Added support for US (m-d-y) and normal (d-m-y) date formats.</li> <li>Build a direct interface to mpeg2encode, allowing users to set speeds of movies from 3-D files.</li>. <li>Added javascript in various places to check and correct user input.</li> <li>Added a framework to incorporate javascript more easily.</li> <li>Cosmetic changes that should make SIDB look more similar in Netscape 6.0 and Opera.</li> </ul>

Scientific Image DataBase

File Release Notes and Changelog

Release Name: 0.17

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