Alida - User contributions [en]

Main Page

2012-03-13T10:10:17Z

Sysop: /* Current release */

== [[News]] ==

* 12/03/2012: The Alida concept now features a prototypical implementation in C++! It supports generic operator execution from command line. Release 0.1 is available now from the download page.

* 02/03/2012: Alida release 1.2 has just been published! You can get the new version in the download section! Main new feature: generic user interface generation for operators to use them from commandline and via a Swing GUI!

== Alida - Advanced Library for Integrated Development of Data Analysis Applications ==

...formerly known as Alida - Automatic Logging of Process Information in Data Analysis

Alida defines a concept for designing libraries and toolkits in data analysis. It supports and simplifies integrated algorithm development by inherently joining algorithm implementation, automatic analysis process documentation and fully generic generation of user interfaces. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoced in a predefined way.

Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.

Alida's operator concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commanline interfaces.

== Licensing information ==
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].

== Current releases ==

==== Java ====
You can download Alida's Java implementation in version 1.2 [[Downloads | here]]. 
You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/java/index.html here]. 

==== C++ ====
You can download Alida's prototypical C++ implementation in version 0.1 [[Downloads | here]]. 
You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/cpp/index.html here]. 

== Manual ==
Alida offers you a user and programmer manual you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here]. Note that the manual is currently focussed on the mature Java implementation, but it will be updated in near future to cover both implementations.

== Bug reports & Feature requests ==
Bug reports and feature requests can be submitted via the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php bugtracking system] or by mail to [mailto:alida@informatik.uni-halle.de alida@informatik.uni-halle.de]. 
Before reporting a new bug, please check if that bug has already been submitted in the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php report list].

Main Page

2012-03-13T10:10:04Z

Sysop: /* Alida - Advanced Library for Integrated Development of data analysis Applications */

== [[News]] ==

* 12/03/2012: The Alida concept now features a prototypical implementation in C++! It supports generic operator execution from command line. Release 0.1 is available now from the download page.

* 02/03/2012: Alida release 1.2 has just been published! You can get the new version in the download section! Main new feature: generic user interface generation for operators to use them from commandline and via a Swing GUI!

== Alida - Advanced Library for Integrated Development of Data Analysis Applications ==

...formerly known as Alida - Automatic Logging of Process Information in Data Analysis

Alida defines a concept for designing libraries and toolkits in data analysis. It supports and simplifies integrated algorithm development by inherently joining algorithm implementation, automatic analysis process documentation and fully generic generation of user interfaces. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoced in a predefined way.

Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.

Alida's operator concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commanline interfaces.

== Licensing information ==
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].

== Current release ==

==== Java ====
You can download Alida's Java implementation in version 1.2 [[Downloads | here]]. 
You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/java/index.html here]. 

==== C++ ====
You can download Alida's prototypical C++ implementation in version 0.1 [[Downloads | here]]. 
You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/cpp/index.html here]. 

== Manual ==
Alida offers you a user and programmer manual you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here]. Note that the manual is currently focussed on the mature Java implementation, but it will be updated in near future to cover both implementations.

== Bug reports & Feature requests ==
Bug reports and feature requests can be submitted via the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php bugtracking system] or by mail to [mailto:alida@informatik.uni-halle.de alida@informatik.uni-halle.de]. 
Before reporting a new bug, please check if that bug has already been submitted in the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php report list].

Downloads

2012-03-13T10:08:19Z

Sysop: /* Manual */

= Java implementation =

== Requirements ==
Alida's implementation in Java requires Java 1.6 or later.

The following external jars are needed to use Alida:

* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
* [http://xstream.codehaus.org/ XStream], Version 1.3.1
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05

In addition, Alida requires some more libraries which are either in-house developments or result from modifications of other libraries:

* We use a slightly modified version of [http://http://sezpoz.java.net/ SezPoz] for annotation indexing. You can get the modified version [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/sezpoz-1.9-alida.jar here].
* Alida also requires some graphml extensions to be found in '''''aldgraphml.jar''''' [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/aldgraphml.jar jar].
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System], the corresponding '''Alida-Help.jar''' can be found [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida-Help.jar here].

If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile. Make sure that all of them are in the classpath when executing the operator runners. 

== Current release (v1.2)==
* Alida Java Binaries [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin.zip zip] (includes Alida binaries, license information and the file ''aldgraphml.jar'' with Alida's extensions of graphml)
* Alida Java Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src.zip zip] (includes only the sources, license files and some READMEs on how to use and compile Alida)
* Alida Java API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api.zip zip] (includes Javadocs of Alida's API)
 

== Archive of Alida's Java releases ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Binaries
! Sources
! API
! Date
|-
| 1.2
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]
| March 2nd, 2012
|-
| 1.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]
| Sep 14th, 2011
|-
| 1.0
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]
| May 9th, 2011
|}
 

= C++ implementation =

Alida's implementation in C++ requires Linux as operating system.

The following external libraries are needed:

* [http://loki-lib.sourceforge.net/index.php?n=Main.HomePage Loki], Version 0.17

Optionally a prototypical implementation of an OpenCV wrapper is included for which the OpenCV library is required:
* [http://opencv.willowgarage.com/wiki/ OpenCV], Version 2.1 or higher (refer to the [[Installation]] section for details on compiling the OpenCV wrapper)

== Current release (v0.1)==
* Alida C++ Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_src.zip zip] (includes the sources, license files and some READMEs on how to use and compile Alida)
* Alida C++ API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_api.zip zip] (includes Doxygen documentation of Alida's C++ API)
 

== Archive of Alida's C++ releases ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Sources
! API
! Date
|-
| 0.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_src-0.1.zip zip] [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_src-0.1.tgz tgz]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_api-0.1.zip zip] [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_api-0.1.tgz tgz]
| March 12th, 2012
|}
 

= Manual =

Detailed information about Alida, its API and usage, can be found in the user and programmer manual.

* Alida-Manual, Version 1.3 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf]
 

= Additional resources =

* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.
 
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.

* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'. 
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'. 
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.
 
Download the current release:
[http
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]
Source code for Chipory is available upon request.
 

= Logo =

* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]

Installation

2012-03-12T16:52:19Z

Sysop: /* C++ */

On this page you find install instructions for Alida in C++ and in Java.

== Java ==

Coming soon... for the moment please refer to the manual and the README files included in the archives.

== C++ ==
The C++ implementation of Alida currently works only on Linux machines.
For installing Alida perform the following steps:

# Download the tar or zip archive from the [[Downloads]] section of this website.
# Extract the archive to a directory of your choice which we denote by ''ALIDA_HOME'' in the following.
# Download [http://loki-lib.sourceforge.net/index.php?n=Main.HomePage Loki], i.e. go to the [http://sourceforge.net/projects/loki-lib/files/Loki/ SourceForge project page] and download release 0.1.7 of the Loki library.
# Extract the Loki archive to the folder ''ALIDA_HOME/external''. Alternatively you can extract it somewhere else and set a link to that directory in ''ALIDA_HOME/external''.
# Define an environment variable ''''ALIDA_CPP'''' with the path of your Alida installation, i.e. the path of ''ALIDA_HOME''.
# Enter the directory ''ALIDA_HOME/src'' and type 'make'.
# The demo operator and the command line operator runner will be built. To run the demo operator, enter the directory ''ALIDA_HOME/src/runner/o.<your-machine>'' and execute it with

<pre>./ALDOpRunner DemoOperator intval=4711 doubleval=0.999999 floatval=0.123 stringval="Alida-Cpp"</pre>

==== Optional: include OpenCV demo operator and provider ====

To activate the OpenCV demo you need to have the OpenCV available on your system. Install instructions can be found [http://opencv.willowgarage.com/wiki/InstallGuide here]. 
To build the OpenCV related classes of Alida edit the configuration file ''ALIDA_HOME/src/config.mk''. 
On top of the file you find a configuration section which defines three variables:

<pre>
#############################################################################
# user-specific configuration
#############################################################################

OPENCV_SUPPORT = no
OPENCV_INCLUDE = /usr/include
OPENCV_LIB = /usr/lib
</pre>

Change the value of '''OPENCV_SUPPORT''' to 'yes' and set include and library path variables according to your OpenCV installation. 
Afterwards rebuild Alida by running 'make clean all'. The OpenCV demo operator can be run with
<pre>
./ALDOpRunner DemoOperatorOpenCV inputImg=<example_image> sigma=151
</pre>

Main Page

2012-03-12T14:06:36Z

Sysop: /* News */

== [[News]] ==

* 12/03/2012: The Alida concept now features a prototypical implementation in C++! It supports generic operator execution from command line. Release 0.1 is available now from the download page.

* 02/03/2012: Alida release 1.2 has just been published! You can get the new version in the download section! Main new feature: generic user interface generation for operators to use them from commandline and via a Swing GUI!

== Alida - Advanced Library for Integrated Development of data analysis Applications ==

...formerly known as Alida - Automatic Logging of Process Information in Data Analysis

Alida defines a concept for designing libraries and toolkits in data analysis. It supports and simplifies integrated algorithm development by inherently joining algorithm implementation, automatic analysis process documentation and fully generic generation of user interfaces. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoced in a predefined way.

Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.

Alida's operator concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commanline interfaces.

== Licensing information ==
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].

== Current release ==

==== Java ====
You can download Alida's Java implementation in version 1.2 [[Downloads | here]]. 
You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/java/index.html here]. 

==== C++ ====
You can download Alida's prototypical C++ implementation in version 0.1 [[Downloads | here]]. 
You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/cpp/index.html here]. 

== Manual ==
Alida offers you a user and programmer manual you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here]. Note that the manual is currently focussed on the mature Java implementation, but it will be updated in near future to cover both implementations.

== Bug reports & Feature requests ==
Bug reports and feature requests can be submitted via the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php bugtracking system] or by mail to [mailto:alida@informatik.uni-halle.de alida@informatik.uni-halle.de]. 
Before reporting a new bug, please check if that bug has already been submitted in the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php report list].

Downloads

2012-03-12T13:27:40Z

Sysop: /* Archive of Alida's C++ releases */

= Java implementation =

== Requirements ==
Alida's implementation in Java requires Java 1.6 or later.

The following external jars are needed to use Alida:

* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
* [http://xstream.codehaus.org/ XStream], Version 1.3.1
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05

In addition, Alida requires some more libraries which are either in-house developments or result from modifications of other libraries:

* We use a slightly modified version of [http://http://sezpoz.java.net/ SezPoz] for annotation indexing. You can get the modified version [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/sezpoz-1.9-alida.jar here].
* Alida also requires some graphml extensions to be found in '''''aldgraphml.jar''''' [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/aldgraphml.jar jar].
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System], the corresponding '''Alida-Help.jar''' can be found [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida-Help.jar here].

If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile. Make sure that all of them are in the classpath when executing the operator runners. 

== Current release (v1.2)==
* Alida Java Binaries [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin.zip zip] (includes Alida binaries, license information and the file ''aldgraphml.jar'' with Alida's extensions of graphml)
* Alida Java Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src.zip zip] (includes only the sources, license files and some READMEs on how to use and compile Alida)
* Alida Java API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api.zip zip] (includes Javadocs of Alida's API)
 

== Archive of Alida's Java releases ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Binaries
! Sources
! API
! Date
|-
| 1.2
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]
| March 2nd, 2012
|-
| 1.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]
| Sep 14th, 2011
|-
| 1.0
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]
| May 9th, 2011
|}
 

= C++ implementation =

Alida's implementation in C++ requires Linux as operating system.

The following external libraries are needed:

* [http://loki-lib.sourceforge.net/index.php?n=Main.HomePage Loki], Version 0.17

Optionally a prototypical implementation of an OpenCV wrapper is included for which the OpenCV library is required:
* [http://opencv.willowgarage.com/wiki/ OpenCV], Version 2.1 or higher (refer to the [[Installation]] section for details on compiling the OpenCV wrapper)

== Current release (v0.1)==
* Alida C++ Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_src.zip zip] (includes the sources, license files and some READMEs on how to use and compile Alida)
* Alida C++ API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_api.zip zip] (includes Doxygen documentation of Alida's C++ API)
 

== Archive of Alida's C++ releases ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Sources
! API
! Date
|-
| 0.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_src-0.1.zip zip] [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_src-0.1.tgz tgz]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_api-0.1.zip zip] [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_api-0.1.tgz tgz]
| March 12th, 2012
|}
 

= Manual =

Detailed information about Alida, its API and usage, can be found in the user and programmer manual.

* Alida-Manual, Version 1.0 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf]
 

= Additional resources =

* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.
 
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.

* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'. 
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'. 
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.
 
Download the current release:
[http
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]
Source code for Chipory is available upon request.
 

= Logo =

* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]

Downloads

2012-03-12T13:27:14Z

Sysop: /* Archive of Alida's C++ releases */

= Java implementation =

== Requirements ==
Alida's implementation in Java requires Java 1.6 or later.

The following external jars are needed to use Alida:

* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
* [http://xstream.codehaus.org/ XStream], Version 1.3.1
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05

In addition, Alida requires some more libraries which are either in-house developments or result from modifications of other libraries:

* We use a slightly modified version of [http://http://sezpoz.java.net/ SezPoz] for annotation indexing. You can get the modified version [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/sezpoz-1.9-alida.jar here].
* Alida also requires some graphml extensions to be found in '''''aldgraphml.jar''''' [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/aldgraphml.jar jar].
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System], the corresponding '''Alida-Help.jar''' can be found [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida-Help.jar here].

If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile. Make sure that all of them are in the classpath when executing the operator runners. 

== Current release (v1.2)==
* Alida Java Binaries [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin.zip zip] (includes Alida binaries, license information and the file ''aldgraphml.jar'' with Alida's extensions of graphml)
* Alida Java Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src.zip zip] (includes only the sources, license files and some READMEs on how to use and compile Alida)
* Alida Java API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api.zip zip] (includes Javadocs of Alida's API)
 

== Archive of Alida's Java releases ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Binaries
! Sources
! API
! Date
|-
| 1.2
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]
| March 2nd, 2012
|-
| 1.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]
| Sep 14th, 2011
|-
| 1.0
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]
| May 9th, 2011
|}
 

= C++ implementation =

Alida's implementation in C++ requires Linux as operating system.

The following external libraries are needed:

* [http://loki-lib.sourceforge.net/index.php?n=Main.HomePage Loki], Version 0.17

Optionally a prototypical implementation of an OpenCV wrapper is included for which the OpenCV library is required:
* [http://opencv.willowgarage.com/wiki/ OpenCV], Version 2.1 or higher (refer to the [[Installation]] section for details on compiling the OpenCV wrapper)

== Current release (v0.1)==
* Alida C++ Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_src.zip zip] (includes the sources, license files and some READMEs on how to use and compile Alida)
* Alida C++ API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_api.zip zip] (includes Doxygen documentation of Alida's C++ API)
 

== Archive of Alida's C++ releases ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Sources
! API
! Date
|-
| 0.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_src-0.1.zip zip][http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_src-0.1.tgz tgz]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_api-0.1.zip zip][http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_api-0.1.tgz tgz]
| March 12th, 2012
|}
 

= Manual =

Detailed information about Alida, its API and usage, can be found in the user and programmer manual.

* Alida-Manual, Version 1.0 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf]
 

= Additional resources =

* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.
 
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.

* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'. 
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'. 
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.
 
Download the current release:
[http
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]
Source code for Chipory is available upon request.
 

= Logo =

* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]

Downloads

2012-03-12T13:26:45Z

Sysop: /* Archive of Alida's C++ releases */

= Java implementation =

== Requirements ==
Alida's implementation in Java requires Java 1.6 or later.

The following external jars are needed to use Alida:

* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
* [http://xstream.codehaus.org/ XStream], Version 1.3.1
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05

In addition, Alida requires some more libraries which are either in-house developments or result from modifications of other libraries:

* We use a slightly modified version of [http://http://sezpoz.java.net/ SezPoz] for annotation indexing. You can get the modified version [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/sezpoz-1.9-alida.jar here].
* Alida also requires some graphml extensions to be found in '''''aldgraphml.jar''''' [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/aldgraphml.jar jar].
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System], the corresponding '''Alida-Help.jar''' can be found [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida-Help.jar here].

If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile. Make sure that all of them are in the classpath when executing the operator runners. 

== Current release (v1.2)==
* Alida Java Binaries [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin.zip zip] (includes Alida binaries, license information and the file ''aldgraphml.jar'' with Alida's extensions of graphml)
* Alida Java Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src.zip zip] (includes only the sources, license files and some READMEs on how to use and compile Alida)
* Alida Java API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api.zip zip] (includes Javadocs of Alida's API)
 

== Archive of Alida's Java releases ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Binaries
! Sources
! API
! Date
|-
| 1.2
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]
| March 2nd, 2012
|-
| 1.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]
| Sep 14th, 2011
|-
| 1.0
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]
| May 9th, 2011
|}
 

= C++ implementation =

Alida's implementation in C++ requires Linux as operating system.

The following external libraries are needed:

* [http://loki-lib.sourceforge.net/index.php?n=Main.HomePage Loki], Version 0.17

Optionally a prototypical implementation of an OpenCV wrapper is included for which the OpenCV library is required:
* [http://opencv.willowgarage.com/wiki/ OpenCV], Version 2.1 or higher (refer to the [[Installation]] section for details on compiling the OpenCV wrapper)

== Current release (v0.1)==
* Alida C++ Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_src.zip zip] (includes the sources, license files and some READMEs on how to use and compile Alida)
* Alida C++ API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_api.zip zip] (includes Doxygen documentation of Alida's C++ API)
 

== Archive of Alida's C++ releases ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Sources
! API
! Date
|-
| 0.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-Cpp_src-0.1.zip zip][http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-Cpp_src-0.1.tgz tgz]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-Cpp_api-0.1.zip zip][http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-Cpp_api-0.1.tgz tgz]
| March 12th, 2012
|}
 

= Manual =

Detailed information about Alida, its API and usage, can be found in the user and programmer manual.

* Alida-Manual, Version 1.0 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf]
 

= Additional resources =

* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.
 
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.

* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'. 
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'. 
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.
 
Download the current release:
[http
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]
Source code for Chipory is available upon request.
 

= Logo =

* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]

Downloads

2012-03-12T13:26:09Z

Sysop: /* Archive of Alida's C++ releases */

= Java implementation =

== Requirements ==
Alida's implementation in Java requires Java 1.6 or later.

The following external jars are needed to use Alida:

* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
* [http://xstream.codehaus.org/ XStream], Version 1.3.1
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05

In addition, Alida requires some more libraries which are either in-house developments or result from modifications of other libraries:

* We use a slightly modified version of [http://http://sezpoz.java.net/ SezPoz] for annotation indexing. You can get the modified version [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/sezpoz-1.9-alida.jar here].
* Alida also requires some graphml extensions to be found in '''''aldgraphml.jar''''' [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/aldgraphml.jar jar].
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System], the corresponding '''Alida-Help.jar''' can be found [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida-Help.jar here].

If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile. Make sure that all of them are in the classpath when executing the operator runners. 

== Current release (v1.2)==
* Alida Java Binaries [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin.zip zip] (includes Alida binaries, license information and the file ''aldgraphml.jar'' with Alida's extensions of graphml)
* Alida Java Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src.zip zip] (includes only the sources, license files and some READMEs on how to use and compile Alida)
* Alida Java API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api.zip zip] (includes Javadocs of Alida's API)
 

== Archive of Alida's Java releases ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Binaries
! Sources
! API
! Date
|-
| 1.2
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]
| March 2nd, 2012
|-
| 1.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]
| Sep 14th, 2011
|-
| 1.0
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]
| May 9th, 2011
|}
 

= C++ implementation =

Alida's implementation in C++ requires Linux as operating system.

The following external libraries are needed:

* [http://loki-lib.sourceforge.net/index.php?n=Main.HomePage Loki], Version 0.17

Optionally a prototypical implementation of an OpenCV wrapper is included for which the OpenCV library is required:
* [http://opencv.willowgarage.com/wiki/ OpenCV], Version 2.1 or higher (refer to the [[Installation]] section for details on compiling the OpenCV wrapper)

== Current release (v0.1)==
* Alida C++ Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_src.zip zip] (includes the sources, license files and some READMEs on how to use and compile Alida)
* Alida C++ API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_api.zip zip] (includes Doxygen documentation of Alida's C++ API)
 

== Archive of Alida's C++ releases ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Sources
! API
! Date
|-
| 0.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-0.1.zip zip][http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-0.1.tgz tgz]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-0.1.zip zip][http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-0.1.tgz tgz]
| March 12th, 2012
|}
 

= Manual =

Detailed information about Alida, its API and usage, can be found in the user and programmer manual.

* Alida-Manual, Version 1.0 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf]
 

= Additional resources =

* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.
 
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.

* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'. 
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'. 
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.
 
Download the current release:
[http
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]
Source code for Chipory is available upon request.
 

= Logo =

* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]

Downloads

2012-03-12T13:25:34Z

Sysop:

= Java implementation =

== Requirements ==
Alida's implementation in Java requires Java 1.6 or later.

The following external jars are needed to use Alida:

* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
* [http://xstream.codehaus.org/ XStream], Version 1.3.1
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05

In addition, Alida requires some more libraries which are either in-house developments or result from modifications of other libraries:

* We use a slightly modified version of [http://http://sezpoz.java.net/ SezPoz] for annotation indexing. You can get the modified version [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/sezpoz-1.9-alida.jar here].
* Alida also requires some graphml extensions to be found in '''''aldgraphml.jar''''' [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/aldgraphml.jar jar].
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System], the corresponding '''Alida-Help.jar''' can be found [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida-Help.jar here].

If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile. Make sure that all of them are in the classpath when executing the operator runners. 

== Current release (v1.2)==
* Alida Java Binaries [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin.zip zip] (includes Alida binaries, license information and the file ''aldgraphml.jar'' with Alida's extensions of graphml)
* Alida Java Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src.zip zip] (includes only the sources, license files and some READMEs on how to use and compile Alida)
* Alida Java API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api.zip zip] (includes Javadocs of Alida's API)
 

== Archive of Alida's Java releases ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Binaries
! Sources
! API
! Date
|-
| 1.2
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]
| March 2nd, 2012
|-
| 1.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]
| Sep 14th, 2011
|-
| 1.0
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]
| May 9th, 2011
|}
 

= C++ implementation =

Alida's implementation in C++ requires Linux as operating system.

The following external libraries are needed:

* [http://loki-lib.sourceforge.net/index.php?n=Main.HomePage Loki], Version 0.17

Optionally a prototypical implementation of an OpenCV wrapper is included for which the OpenCV library is required:
* [http://opencv.willowgarage.com/wiki/ OpenCV], Version 2.1 or higher (refer to the [[Installation]] section for details on compiling the OpenCV wrapper)

== Current release (v0.1)==
* Alida C++ Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_src.zip zip] (includes the sources, license files and some READMEs on how to use and compile Alida)
* Alida C++ API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_api.zip zip] (includes Doxygen documentation of Alida's C++ API)
 

== Archive of Alida's C++ releases ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Sources
! API
! Date
|-
| 0.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip][http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.tgz tgz]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip][http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.tgz tgz]
| March 12th, 2012
|}
 

= Manual =

Detailed information about Alida, its API and usage, can be found in the user and programmer manual.

* Alida-Manual, Version 1.0 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf]
 

= Additional resources =

* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.
 
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.

* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'. 
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'. 
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.
 
Download the current release:
[http
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]
Source code for Chipory is available upon request.
 

= Logo =

* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]

MediaWiki:Sidebar

2012-03-09T16:21:36Z

Sysop:

* navigation
** mainpage|mainpage-description
** Downloads|Downloads
** Installation|Installation
** Quickstart|Quickstart and Code Examples
** Projects|Related Projects and Publications
** Recent_changes|Recent Changes
** Acknowledge|Acknowledgements
** Alida:About|Imprint
* documentation
** features|Features
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Quickstart

2012-03-09T16:19:19Z

Sysop:

Here we introduce Alida's operator concept with some code snippets to give you a first impression of how to deal with Alida on the programming level.

* for Java snippets and more follow [[Java_quick|this]] link
* C++ snippets and interesting information on the implementation in C++ can be found [[C++_quick|here]]

Notes on the installation of Alida can be found [[Installation|here]] and in the user manual accessible from [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here].

Java quick

2012-03-09T16:17:35Z

Sysop: Created page with "Here we introduce Alida's operator concept with some code snippets of <code>ALDOperator</code> and sub-classed demo operators. we focus on Alida's capabilities to automatically g..."

Here we introduce Alida's operator concept with some code snippets of <code>ALDOperator</code> and sub-classed demo operators.
we focus on Alida's capabilities to automatically generate user interfaces.

= First operator =

As a first example of an Alida operator we implement the row or column wise
sum for a 2D array of Doubles.
The class <code>MatrixSum</code> extending <code>ALDOperator</code> features three member variables
holding the input 2D array, an enum to indicate the mode of summation (<code>ROW</code> or <code>COLUMN</code>), and
an 1D array of the sums to be computed and returned by the operator.
Alida requires only to annotate these members with the @Parameter annotation
which declares

* the direction (<code>IN</code>, <code>OUT</code>, <code>INOUT</code>),
* whether the parameter is required,
* an optional textual description,
* and a label used, e.g. in the graphical user interface automatically generated
to execute the operator.

It is important to add a public standard constructor (without arguments)
to be able to use Java's reflection mechanism.
Finally, the abstract method <code>operate()</code> of <code>ALDOperator</code> has to be overridden
implementing the functionality of the operator.

<pre>
@ALDAOperator(genericExecutionMode=ALDAOperator.ExecutionMode.ALL,
level=ALDAOperator.Level.APPLICATION)
public class MatrixSum extends ALDOperator {

/** Choose row or colum wise sum
*/
public static enum SummarizeMode {
/** row wise */
ROW,

/** column wise */
COLUMN
}

/**
* Input matrix
*/
@Parameter( label= "Input matrix", required = true,
direction = Parameter.Direction.IN, description = "Input matrix.")
private Double[][] matrix;

/**
* Mode of summarizing
*/
@Parameter( label= "Summarize mode", required = true,
direction = Parameter.Direction.IN, description = "Sum over columns or rows?")
private SummarizeMode summarizeMode = SummarizeMode.ROW;

/**
* 1D Array of sums.
*/
@Parameter( label= "sums",
direction = Parameter.Direction.OUT, description = "Row or column wise sums.")
private Double[] sums = null;

/**
* Default constructor.
* @throws ALDOperatorException
*/
public MatrixSum() throws ALDOperatorException {
}

/**
* Constructor.
*
* @param matrix Input matrix.
* @throws ALDOperatorException
*/
public MatrixSum(Double[] [] matrix) throws ALDOperatorException {
this.matrix = matrix;
}

@Override
protected void operate() {
if ( matrix == null )
sums = null;

// calculate sums
if ( summarizeMode == SummarizeMode.ROW ) {
sums = new Double[matrix.length];
for ( int row = 0 ; row < matrix.length ; row++ ) {
sums[row] = 0.0;
for ( int col = 0 ; col < matrix[0].length ; col++ )
sums[row] += matrix[row][col];
}
} else {
sums = new Double[matrix[0].length];
for ( int col = 0 ; col < matrix[0].length ; col++ ) {
sums[col] = 0.0;
for ( int row = 0 ; row < matrix.length ; row++ )
sums[col] += matrix[row][col];
}
}
}
</pre>

These are the basic requirements for the operator to be used on the programming level.
An example of this use is included in the example in the next section.

If we further annotate the class with
<pre>
@ALDAOperator(genericExecutionMode=ALDAOperator.ExecutionMode.ALL)
</pre>
this is all needed to also facilitate
execution of this operator via a graphical and a command line user interface
automatically generated by Alida.
(Setting <code>level=ALDAOperator.Level.APPLICATION</code> declares this operator an application
which is used in the GUI to control display of available operators.)

== Invocation via a graphical user interface ==

Alida comes with one single application to execute Alida operators
with a automatically generated graphical user interface which may be
started from command line by
<pre>
java de.unihalle.informatik.Alida.tools.ALDOpRunnerGUI
</pre>

This will pop up a window to choose an operator to execute.
Arranged according to the package structure all operators allows to be executed
via the graphical user interface according to their <code>genericExecutionMode</code>
are displayed.
Initially packages are unfolded up to a predefined depth.
Unfold the demo package, select <code>MatrixSum</code>, and choose the "Configure Operator" button.
This will pop up another window which allows you to configure the input parameters
of the operator.
Important note: After finishing to input the data matrix entering the final matrix elements
you have to select a previous matrix element due to subtle AWT details.
For the enumeration to select the mode Alida has automatically generated
a combo box to allow convenient selections.
If you are finished with the parameter configuration you want to invoke the operator
using the run button.
On completion of <code>MatrixSum</code> the interface will pop up the result window which allows you
to inspect the outcome of the operation.

== Invocation via command line ==

The command line user interface of Alida allows to invoke all Alida operator
properly annotated to allows generic execution.

You may invoke the matrix summation operator by
<pre>
java de.unihalle.informatik.Alida.tools.ALDOpRunner MatrixSum matrix='[[1,2,3],[4,5,6]]' sums=-
</pre>
which returns as result on standard output
<pre>
sums = [6.0,15.0]
</pre>

Parameter values are specified as name=value pairs.
Alida's syntax for 2D array should be self-explanatory from this example.
As the mode of summation is not supplied as a parameter its default is used

Note, the command
<pre>
java de.unihalle.informatik.Alida.tools.ALDOpRunner MatrixSum matrix='[[1,2,3],[4,5,6]]'
</pre>
will return no output as the command line user interface returns only output parameters requested.

The enumeration defined in <code>MatrixSum</code> is supported by the
user interface without further action required as shown in the next example.
This also demonstrates redirection of output
to a file, sums.out in this case.

<pre>
java de.unihalle.informatik.Alida.tools.ALDOpRunner MatrixSum matrix='[[1,2,3],[4,5,6]]'
summarizeMode=COLUMN sums=@sums.out+
</pre>
Input can be read from file as well:
<pre>
java de.unihalle.informatik.Alida.tools.ALDOpRunner MatrixSum matrix=@data sums=-+
</pre>

where the file data contains the string defining the matrix, e.g., <code>[[1,2,3],[4,5,6]]</code>

= Adding more features to an operator =

We now generalize this example to realize not only summation over rows or
columns, but arbitrary summarizing operations.
This shows Alida's feature to allow an operator as parameter of another operator.

== Implementation ==

First we generalize <code>ALDArraySum</code> to the operator <code>ApplyToMatrix</code>
which also takes a 2D array and an enum indicating the mode of marginalization (<code>ROW</code> or <code>COLUMN</code>).
It takes an additional input parameter which specifies the operation to be applied on each
row or column.

This parameter is itself an Alida operator and of type <code>ALDSummarizeArrayOp</code>
which is implemented as an abstract class.
This abstract operator defines a summarizing operator
which takes a 1D array as input and returns a summarizing scalar.
As this is an abstract class there is no need to override the <code>operate()</code>
method, however some getter and setter methods are provided.

<pre>
@Parameter( label= "Input 1D array", required = true,
direction = Parameter.Direction.IN, description = "Input array (1D).")
protected Double[] data;

/**
* Summarizing scalar
*/
@Parameter( label= "Summarizing scalar",
direction = Parameter.Direction.OUT, description = "Summarizing scalar of the 1D arra")
protected Double summary = null;

/**
* Default constructor.
* @throws ALDOperatorException
*/
public ALDSummarizeArrayOp() throws ALDOperatorException {
}

/**
* Returns the 1D array
* @return data array
*/
public Double[] getData() {
return this.data;
}

/**
* Sets the 1D array
* @param data
*/
public void setData( Double[] data) {
this.data = data;
}

</pre>

Now we add concrete examples of such a summarizing operation, in this case
summation (<code>ALDArraySum</code>), to return the mean (<code>ALDArrayMean</code>), and the minimum (<code>ALDArrayMin</code>).
Each implements the <code>operate()</code> method and has to supply a standard constructor.
In this example we add another constructor for convenience.
This operators are declared as operators on the standard in contrast to
application level, as they are not expected to be invoked as an application.
However, setting the level to standard in the menu of the graphical user interface
stills allows their execution.
When extending the abstract super class it is necessary to annotate the
class with <code>@ALDDerivedClass</code> in order to allow Alida's dataIO mechanism to find the derived class
in the automatically generated user interface.
This holds for other parameter types as well.
More specifically, if an instance of a class is to be supplied in an automatically
generated user interface as a value for a parameter of one of its super classes,
Alida requires the annotation <code>@ALDDerivedClass</code>.

<pre>
@ALDDerivedClass
@ALDAOperator(genericExecutionMode=ALDAOperator.ExecutionMode.ALL,
level=ALDAOperator.Level.STANDARD)
public class ALDArraySum extends ALDSummarizeArrayOp {

@Override
protected void operate() {
summary = 0.0;
for ( int i = 0 ; i < data.length ; i++ )
summary += data[i];
}

/**
* Default constructor.
* @throws ALDOperatorException
*/
public ALDArraySum() throws ALDOperatorException {
}

</pre>

Now we are ready to implement
the <code>ApplyToMatrix</code> operator, which also demonstrates supplemental parameters.
This supplementals, e.g., control debugging output or returning of intermediate results.
For demo purposes we declare a supplemental input parameter <code>returnElapsedTime</code>.
If it is set to true the operator will return the elapsed time in a second
supplemental parameter with direction output.

Again, the operation is implemented in the <code>operate()</code> method and the remainder of the
class supplies getter and setter methods for convenience.
The <code>operate()</code> method give also an example of the invocation of an operator on the
programming level.
In this case, an instance of the operator is already passed as a parameter.
Its parameters are set, in this case each 1D array to be summarized in turn.
Upon return from the method <code>runOp()</code> the results may be retrieved from the operator object,
in this example with the <code>getSummary()</code> method.
Besides getter and setter methods as implemented in each operator
Alida provides also a generic get and set methods applicable to
all parameters of an operator.
Note, that the operator is not invoked by its <code>operate()</code> method, but via
the <code>runOp()</code> method implemented the base class <code>ALDOperator</code>.
This methods validates the parameters before invocation of <code>operate()</code>.
Furthermore, it take all necessary measures for Alida's processing
history which automatically logs
all manipulative actions on the data and corresponding parameter settings.

<pre>
@ALDAOperator(genericExecutionMode=ALDAOperator.ExecutionMode.ALL,
level=ALDAOperator.Level.APPLICATION)
public class ApplyToMatrix extends ALDOperator {

/** Choose row or colum wise sum
*/
public static enum SummarizeMode {
/** row wise */
ROW,
/** column wise */
COLUMN
}

/**
* Input matrix
*/
@Parameter( label= "Input matrix", required = true,
direction = Parameter.Direction.IN, description = "Input matrix.")
private Double[][] matrix;

/**
* Mode of summarizing
*/
@Parameter( label= "Summarize mode", required = true,
direction = Parameter.Direction.IN, description = "Sum over columns or rows.")
private SummarizeMode summarizeMode = SummarizeMode.ROW;

/**
* Summarizing opererator
*/
@Parameter( label= "Summarizing operator", required = true,
direction = Parameter.Direction.IN, description = "Specifies the summarizing operation to apply")
private ALDSummarizeArrayOp summarizeOp;

/**
* 1D Array of summaries.
*/
@Parameter( label= "summaries",
direction = Parameter.Direction.OUT, description = "Row or column wise summaries")
private Double[] summaries = null;

/**
* Supplemental to request elapsed time to be returned
*/
@Parameter( label= "Return elapsed time",
direction = Parameter.Direction.IN, description = "Request elapsed time consumed to be returned",
supplemental=true)
private boolean returnElapsedTime = false;

/**
* Elpased time
*/
@Parameter( label= "Elapsed time",
direction = Parameter.Direction.OUT, description = "Elapsed time of operation in milliseconds",
supplemental=true)
private long elapsedTime;

/**
* Default constructor.
* @throws ALDOperatorException
*/
public ApplyToMatrix() throws ALDOperatorException {
}

/**
* Constructor.
*
* @param matrix Input matrix.
* @throws ALDOperatorException
*/
public ApplyToMatrix(Double[] [] matrix) throws ALDOperatorException {
this.matrix = matrix;
}

@Override
protected void operate() throws ALDOperatorException,ALDProcessingDAGException {
if ( returnElapsedTime )
elapsedTime = System.currentTimeMillis();

if ( matrix == null )
summaries = null;

// calculate summaries
if ( summarizeMode == SummarizeMode.ROW ) {
summaries = new Double[matrix.length];
for ( int row = 0 ; row < matrix.length ; row++ ) {
summarizeOp.setData(matrix[row]);
summarizeOp.runOp();
summaries[row] = summarizeOp.getSummary();
}
} else {
summaries = new Double[matrix[0].length];
Double[] tmp = new Double[matrix.length];
for ( int col = 0 ; col < matrix[0].length ; col++ ) {
for ( int row = 0 ; row < matrix.length ; row++ )
tmp[row] = matrix[row][col];

summarizeOp.setData(tmp);
summarizeOp.runOp();
summaries[col] = summarizeOp.getSummary();
}
}

if ( returnElapsedTime )
elapsedTime = System.currentTimeMillis() - elapsedTime;
}

// ==============================================================
// Getter and setter methods
/** Get value of returnElapsedTime.
* Explanation: Request elapsed time consumed to be returned.
* @return value of returnElapsedTime
*/
public boolean getReturnElapsedTime(){
return returnElapsedTime;
}

/** Set value of returnElapsedTime.
* Explanation: Request elapsed time consumed to be returned.
* @param value New value of returnElapsedTime
*/
public void setReturnElapsedTime( boolean value){
this.returnElapsedTime = value;
}
</pre>

== Invocation via a graphical user interface ==

If the graphical interface is still running just select our new operator
and begin to configure it.
For the parameter summarizing operator you have a choice of all operators extending
the abstract operator <code>ALDSummarizeArrayOp</code>.
All which is necessary on the implementation side is proper annotation of the extending
classes with <code>@ALDDerivedClass</code>.
As the selected operator may have its own parameters you may want to configure it.
In our example this is not necessary as the input array is, of course, supplied
by the <code>ApplyToMatrix</code> operator.
Do not forget to input your data before hitting the run button.
After return, again a result window give you the results of the operation.
Note, if you did not tick Return elapsed time" this window will show zero
for the time elapsed as the operator has not been request to stop the time.

== Invocation via command line ==

When invoking the <code>ApplyToMatrix</code> operator from command line
we have to handle derived classes as value for parameters.
In the graphical user interface Alida features a combo box where
we may choose from.
In the command line interface Alida allows to prefix the value of a parameter
with a derived class to be passed to the operator.
This is necessary as Alida as, of course, no way to itself
decide if and which derived class is to be used.
Alida's syntax is to enclose the class name in a dollar sign and a colon.
As evident in the following example, abbreviations are of the fully
qualified class name are accepted as long as they are unambiguous.
<pre>
java de.unihalle.informatik.Alida.tools.ALDOpRunner Apply \
matrix='[[1,2,3],[4,5,6]]' \
summarizeMode=ROW \
summarizeOp='<math>ALDArrayMean:{}' \
summaries=-
</pre>
results in
<pre>
summaries = [2.0,5.0]
</pre>

<code>ALDOpRunner</code> may be persuaded to show all operators derived from <code>ALDSummarizeArrayOp</code>
and known within the user interface if we enter an invalid class name:
<pre>
java de.unihalle.informatik.Alida.tools.ALDOpRunner \
Apply matrix='[[1,2,3],[4,5,6]]' \
summarizeMode=ROW summarizeOp='</math>dd:{}' \
summaries=-
</pre>
yields
<pre>
ALDStandardizedDataIOCmdline::readData found 0 derived classes matching <dd>
derived classes available:
de.unihalle.informatik.Alida.demo.ALDArrayMean
de.unihalle.informatik.Alida.demo.ALDArrayMin
de.unihalle.informatik.Alida.demo.ALDArraySum
ERROR: reading parameter <summarizeOp> returns null
</pre>

Supplemental parameters are handled like other parameters
<pre>
java de.unihalle.informatik.Alida.tools.ALDOpRunner Apply \
matrix='[[1,2,3],[4,5,6]]' \
summarizeMode=COLUMN \
summarizeOp='<math>ALDArrayMin:{}' \
summaries=- \
returnElapsedTime=true \
elapsedTime=-
</pre>
gives
<pre>
summaries = [1.0,2.0,3.0]
elapsedTime = 4
</pre>

= Adding more data types as parameters =

Alida provides automatic IO of primitive data types, enumerations, arrays, collections,
and operators.
In addition so called parameterized classes are supported.
Any Java class may be declared to be a parameterized class in Alida
by annotating the class <code>@ALDParametrizedClass</code> as shown in the
class <code>ExperimentalData</code>.
All member variables to be known to and handled by Alida's user interface
simply need to be annotated with <code>@ALDClassParameter</code>.

Here we implement a toy version of experimental data <code>ExperimentalData</code>.
A complete experiment consists of a number of independent repetitions of
sub experiments.
In each of these the same features (measurements) are recorded.
The measurements a represented in
a 2D array of Doubles, where each column represents
one sub experiment and the rows the distinct features.
The measurements may be normalized which is indicated by the
normalized member variable.

The class is annotated by <code>@ALDParametrizedClass</code>, and
and all members to be handle in Alida'a user interfaces are
to be annotated with <code>@ALDParametrizedClass</code>.
The label field has the same semantics as for parameters of operators.
These annotations are the only implementational overhead
to allow Alida to automatically generate user interfaces
where the parameterized class acts a a parameter.

<pre>
@ALDParametrizedClass
@ALDMetaInfo(export=ALDMetaInfo.ExportPolicy.MANDATORY)
public class ExperimentalData {
@ALDClassParameter(label="description")
private String description = null;

@ALDClassParameter(label="data")
private Double[][] data = null;

/** are the data normalized
*/
@ALDClassParameter(label="Is normalized")
private boolean normalized = false;

/** Standard constructor is needed
*/
public ExperimentalData() {
}

/** Constructor for an experiment.
* Normalized is assumed to be false.
*
* @param description a textual desciption of the experiment
* @param data measurements
*/
public ExperimentalData( String description, Double[][] data) {
this( description, data, false);
}

/** Constructor for an experiment.
*
* @param description a textual desciption of the experiment
* @param data measurements
* @param normalized are the data normalized
*/
public ExperimentalData( String description, Double[][] data, boolean normalized) {
this.normalized = normalized;
this.description = description;
this.setData( data, normalized);
}
</pre>

This is shown below for a simple normalizing operator <code>NormalizeExperimentalDataOp</code>
which takes experimental data as input an returns a new instance
of <code>ExperimentalData</code> which contains normalized data.

<pre>
@ALDAOperator(genericExecutionMode=ALDAOperator.ExecutionMode.ALL,
level=ALDAOperator.Level.APPLICATION)
public class NormalizeExperimentalDataOp extends ALDOperator {

/**
* Input data
*/
@Parameter( label= "Experimental data", required = true,
direction = Parameter.Direction.IN, description = "Experimental data to be normalized")
private ExperimentalData experiment = null;

/**
* Normalized experiment to be returned
*/
@Parameter( label= "Normalized experiment",
direction = Parameter.Direction.OUT, description = "Normalized experiment")
private ExperimentalData result = null;

/**
* Default constructor.
* @throws ALDOperatorException
*/
public NormalizeExperimentalDataOp() throws ALDOperatorException {
}

/**
* Constructor.
*
* @param experiment Experimental data
* @throws ALDOperatorException
*/
public NormalizeExperimentalDataOp(ExperimentalData experiment) throws ALDOperatorException {
this.experiment = experiment;
}

@Override
protected void operate() throws ALDOperatorException,ALDProcessingDAGException {

ApplyToMatrix normalizeOp = new ApplyToMatrix( experiment.getData());
normalizeOp.setSummarizeMode( ApplyToMatrix.SummarizeMode.ROW);
normalizeOp.setSummarizeOp( new ALDArrayMean());
normalizeOp.runOp();

Double[][] normalizedData = (Double[][])(experiment.getData().clone());
for ( int e = 0; e < experiment.getNumExperiments(); e++ ) {
for ( int f = 0 ; f < experiment.getNumFeatures() ; f++ ) {
normalizedData[f][e] -= normalizeOp.getSummaries()[f];
}
}

result = new ExperimentalData( experiment.getDescription() + " (Normalized)", normalizedData, true);
}
</pre>

This mechanism applies in a recursive fashion, i.e. a parameterized class may
(recursively) contain a member variable which itself is a parametrized class.
Likewise, an operator acting as a parameter of another operator
may in turn have a parameter of type <code>ALDOperator</code>.

== Invocation via a graphical user interface ==

Invoking and configuring <code>NormalizeExperimentalDataOp</code> from the graphical user interface
shows as the only required parameter the experimental data.
This parameterized class can be configured in a separate window
very similar to to configuration of operators.
Likewise the resulting normalized experimental data
may be inspected in their own window.

Obviously this is a toy example, as we would not expect the measurements to
be entered manually, but rather stored and read from file in a specialized format.
This is one of the rare cases where
custom data IO provider need to be implemented, in this
case for <code>ExperimentalData</code>.

== Invocation via command line ==

Again, invocation from command line is provided by Alida in an automatic
way with no further implementational overhead.
The syntax for parameterized classes es a comma separated list of name=value pairs
enclosed in curly brackets where name refers to annotated member variables of
the parameterized class.

<pre>
java de.unihalle.informatik.Alida.tools.ALDOpRunner NormalizeExperimentalDataOp \
experiment='{data=[[1,2,3],[2,2,2],[100,103,110]],description="Demo experiment"}' \
result=-
</pre>
yields
<pre>
result = { normalized = true ,
description = "Demo experiment" (Normalized) ,
data = [[-1.0,0.0,1.0],[0.0,0.0,0.0],
[-4.333333333333329,-1.3333333333333286,5.666666666666671]] }
</pre>

If a class derived from <code>ExperimentalData</code> was to be supplied to the operator,
the curly brackets can be prefixed by a derive class definition starting with a dollar sign
and ending with a colon as shown for the summarizing operators above.

Installation

2012-03-09T16:12:00Z

Sysop:

On this page you find install instructions for Alida in C++ and in Java.

== Java ==

Coming soon... for the moment please refer to the manual and the README files included in the archives.

== C++ ==
The C++ implementation of Alida currently works only on Linux machines.
For installing Alida perform the following steps:

# Download the tar or zip archive from the [[Downloads]] section of this website.
# Extract the archive to a directory of your choice which we denote by ''ALIDA_HOME'' in the following.
# Download [http://loki-lib.sourceforge.net/index.php?n=Main.HomePage Loki], i.e. go to the [http://sourceforge.net/projects/loki-lib/files/Loki/ SourceForge project page] and download release 0.1.7 of the Loki library.
# Extract the Loki archive to the folder ''ALIDA_HOME/external''. Alternatively you can extract it somewhere else and set a link to that directory in ''ALIDA_HOME/external''.
# Define an environment variable ''''ALIDA_CPP'''' with the path of your Alida installation, i.e. the path of ''ALIDA_HOME''.
# Enter the directory ''ALIDA_HOME/src'' and type 'make'.
# You will find a demo operator in ''ALIDA_HOME/src/demo/o.<your-machine>''. Enter the directory and run the demo operator with

<pre>./ALDOpRunner DemoOperator intval=4711 doubleval=0.999999 floatval=0.123 stringval="Alida-Cpp"</pre>

==== Optional: include OpenCV demo operator and provider ====

To activate the OpenCV demo you need to have the OpenCV available on your system. Install instructions can be found [http://opencv.willowgarage.com/wiki/InstallGuide here]. 
To build the OpenCV related classes of Alida edit the configuration file ''ALIDA_HOME/src/config.mk''. 
On top of the file you find a configuration section which defines three variables:

<pre>
#############################################################################
# user-specific configuration
#############################################################################

OPENCV_SUPPORT = no
OPENCV_INCLUDE = /usr/include
OPENCV_LIB = /usr/lib
</pre>

Change the value of '''OPENCV_SUPPORT''' to 'yes' and set include and library path variables according to your OpenCV installation. 
Afterwards rebuild Alida by running 'make clean all'. The OpenCV demo operator can be run with
<pre>
./ALDOpRunner DemoOperatorOpenCV inputImg=<example_image> sigma=151
</pre>

Main Page

2012-03-09T16:10:44Z

Sysop: /* News */

== [[News]] ==

* 09/03/2012: The Alida concept now features a prototypical implementation in C++! It supports generic operator execution from command line. Release 0.1 will be available soon for download...

* 02/03/2012: Alida release 1.2 has just been published! You can get the new version in the download section! Main new feature: generic user interface generation for operators to use them from commandline and via a Swing GUI!

== Alida - Advanced Library for Integrated Development of data analysis Applications ==

...formerly known as Alida - Automatic Logging of Process Information in Data Analysis

Alida defines a concept for designing libraries and toolkits in data analysis. It supports and simplifies integrated algorithm development by inherently joining algorithm implementation, automatic analysis process documentation and fully generic generation of user interfaces. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoced in a predefined way.

Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.

Alida's operator concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commanline interfaces.

== Licensing information ==
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].

== Current release ==

==== Java ====
You can download Alida's Java implementation in version 1.2 [[Downloads | here]]. 
You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/java/index.html here]. 

==== C++ ====
You can download Alida's prototypical C++ implementation in version 0.1 [[Downloads | here]]. 
You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/cpp/index.html here]. 

== Manual ==
Alida offers you a user and programmer manual you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here]. Note that the manual is currently focussed on the mature Java implementation, but it will be updated in near future to cover both implementations.

== Bug reports & Feature requests ==
Bug reports and feature requests can be submitted via the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php bugtracking system] or by mail to [mailto:alida@informatik.uni-halle.de alida@informatik.uni-halle.de]. 
Before reporting a new bug, please check if that bug has already been submitted in the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php report list].

Downloads

2012-03-09T16:10:34Z

Sysop:

= Java implementation =

== Requirements ==
Alida's implementation in Java requires Java 1.6 or later.

The following external jars are needed to use Alida:

* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
* [http://xstream.codehaus.org/ XStream], Version 1.3.1
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05

In addition, Alida requires some more libraries which are either in-house developments or result from modifications of other libraries:

* We use a slightly modified version of [http://http://sezpoz.java.net/ SezPoz] for annotation indexing. You can get the modified version [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/sezpoz-1.9-alida.jar here].
* Alida also requires some graphml extensions to be found in '''''aldgraphml.jar''''' [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/aldgraphml.jar jar].
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System], the corresponding '''Alida-Help.jar''' can be found [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida-Help.jar here].

If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile. Make sure that all of them are in the classpath when executing the operator runners. 

== Current release (v1.2)==
* Alida Java Binaries [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin.zip zip] (includes Alida binaries, license information and the file ''aldgraphml.jar'' with Alida's extensions of graphml)
* Alida Java Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src.zip zip] (includes only the sources, license files and some READMEs on how to use and compile Alida)
* Alida Java API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api.zip zip] (includes Javadocs of Alida's API)
 

== Archive of Alida's Java releases ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Binaries
! Sources
! API
! Date
|-
| 1.2
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]
| March 2nd, 2012
|-
| 1.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]
| Sep 14th, 2011
|-
| 1.0
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]
| May 9th, 2011
|}
 

= C++ implementation =

Alida's implementation in C++ requires Linux as operating system.

The following external libraries are needed:

* [http://loki-lib.sourceforge.net/index.php?n=Main.HomePage Loki], Version 0.17

Optionally a prototypical implementation of an OpenCV wrapper is included for which the OpenCV library is required:
* [http://opencv.willowgarage.com/wiki/ OpenCV], Version 2.1 or higher (refer to the [[Installation]] section for details on compiling the OpenCV wrapper)

== Current release (v0.1)==
* Alida C++ Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_src.zip zip] (includes the sources, license files and some READMEs on how to use and compile Alida)
* Alida C++ API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_api.zip zip] (includes Doxygen documentation of Alida's C++ API)
 

== Archive of Alida's C++ releases ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Sources
! API
! Date
|-
| 0.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip coming soon...][http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip coming soon...]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.tgz coming soon...][http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.tgz coming soon...]
| March 12th, 2012
|}
 

= Manual =

Detailed information about Alida, its API and usage, can be found in the user and programmer manual.

* Alida-Manual, Version 1.0 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf]
 

= Additional resources =

* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.
 
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.

* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'. 
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'. 
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.
 
Download the current release:
[http
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]
Source code for Chipory is available upon request.
 

= Logo =

* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]

Main Page

2012-03-09T15:57:13Z

Sysop:

== [[News]] ==

* 09/03/2012: The Alida concept now features a prototypical implementation in C++! It supports generic operator execution from command line. Release 0.1 will be available soon for download...

* 01/03/2012: Alida release 1.2 has just been published! You can get the new version in the download section! Main new feature: generic user interface generation for operators to use them from commandline and via a Swing GUI!

== Alida - Advanced Library for Integrated Development of data analysis Applications ==

...formerly known as Alida - Automatic Logging of Process Information in Data Analysis

Alida defines a concept for designing libraries and toolkits in data analysis. It supports and simplifies integrated algorithm development by inherently joining algorithm implementation, automatic analysis process documentation and fully generic generation of user interfaces. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoced in a predefined way.

Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.

Alida's operator concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commanline interfaces.

== Licensing information ==
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].

== Current release ==

==== Java ====
You can download Alida's Java implementation in version 1.2 [[Downloads | here]]. 
You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/java/index.html here]. 

==== C++ ====
You can download Alida's prototypical C++ implementation in version 0.1 [[Downloads | here]]. 
You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/cpp/index.html here]. 

== Manual ==
Alida offers you a user and programmer manual you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here]. Note that the manual is currently focussed on the mature Java implementation, but it will be updated in near future to cover both implementations.

== Bug reports & Feature requests ==
Bug reports and feature requests can be submitted via the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php bugtracking system] or by mail to [mailto:alida@informatik.uni-halle.de alida@informatik.uni-halle.de]. 
Before reporting a new bug, please check if that bug has already been submitted in the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php report list].

Installation

2012-03-09T07:44:22Z

Sysop: Created page with "On this page you find install instructions for Alida in C++ and in Java. == C++ == The C++ implementation of Alida currently works only on Linux machines. For installing Alida p..."

On this page you find install instructions for Alida in C++ and in Java.

== C++ ==
The C++ implementation of Alida currently works only on Linux machines.
For installing Alida perform the following steps:

# Download the tar or zip archive from the [[Downloads]] section of this website.
# Extract the archive to a directory of your choice which we denote by ''ALIDA_HOME'' in the following.
# Download [http://loki-lib.sourceforge.net/index.php?n=Main.HomePage Loki], i.e. go to the [http://sourceforge.net/projects/loki-lib/files/Loki/ SourceForge project page] and download release 0.1.7 of the Loki library.
# Extract the Loki archive to the folder ''ALIDA_HOME/external''. Alternatively you can extract it somewhere else and set a link to that directory in ''ALIDA_HOME/external''.
# Define an environment variable ''''ALIDA_CPP'''' with the path of your Alida installation, i.e. the path of ''ALIDA_HOME''.
# Enter the directory ''ALIDA_HOME/src'' and type 'make'.
# You will find a demo operator in ''ALIDA_HOME/src/demo/o.<your-machine>''. Enter the directory and run the demo operator with

<pre>./ALDOpRunner DemoOperator intval=4711 doubleval=0.999999 floatval=0.123 stringval="Alida-Cpp"</pre>

=== Optional: include OpenCV demo operator and provider ===

To activate the OpenCV demo you need to have the OpenCV available on your system. Install instructions can be found [http://opencv.willowgarage.com/wiki/InstallGuide here]. 
To build the OpenCV related classes of Alida edit the configuration file ''ALIDA_HOME/src/config.mk''. 
On top of the file you find a configuration section which defines three variables:

<pre>
#############################################################################
# user-specific configuration
#############################################################################

OPENCV_SUPPORT = no
OPENCV_INCLUDE = /usr/include
OPENCV_LIB = /usr/lib
</pre>

Change the value of '''OPENCV_SUPPORT''' to 'yes' and set include and library path variables according to your OpenCV installation. 
Afterwards rebuild Alida by running 'make clean all'. The OpenCV demo operator can be run with
<pre>
./ALDOpRunner DemoOperatorOpenCV inputImg=<example_image> sigma=151
</pre>

MediaWiki:Sidebar

2012-03-09T07:19:01Z

Sysop:

* navigation
** mainpage|mainpage-description
** Downloads|Downloads
** Installation|Installation
** Quickstart|Quickstart and Code Examples
** Projects|Related Projects and Publications
** Recent_changes|Recent Changes
** Acknowledge|Acknowledgements
** Alida:About|Imprint
* documentation
** features|Features
** http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf|Manual
** http://www2.informatik.uni-halle.de/agprbio/alida/api/index.html|Javadoc API
** frequently_asked_questions|FAQs
* development
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php|Bug report
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php|Feature request
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php|Report overview
* SEARCH
* TOOLBOX
* LANGUAGES

MediaWiki:Sidebar

2012-03-02T11:48:26Z

Sysop:

* navigation
** mainpage|mainpage-description
** Quickstart|Quickstart and Code Examples
** Downloads|Downloads
** Projects|Related Projects and Publications
** Recent_changes|Recent Changes
** Acknowledge|Acknowledgements
** Alida:About|Imprint
* documentation
** features|Features
** http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf|Manual
** http://www2.informatik.uni-halle.de/agprbio/alida/api/index.html|Javadoc API
** frequently_asked_questions|FAQs
* development
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php|Bug report
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php|Feature request
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php|Report overview
* SEARCH
* TOOLBOX
* LANGUAGES

Quickstart

2012-03-02T11:47:02Z

Sysop:

Here we introduce Alida's operator concept with some code snippets of <code>ALDOperator</code>s
and focus on Alida's capabilities to automatically generate user interfaces.

= First operator =

As a first example of an Alida operator we implement the row or column wise
sum for a 2D array of Doubles.
The class <code>MatrixSum</code> extending <code>ALDOperator</code> features three member variables
holding the input 2D array, an enum to indicate the mode of summation (<code>ROW</code> or <code>COLUMN</code>), and
an 1D array of the sums to be computed and returned by the operator.
Alida requires only to annotate these members with the @Parameter annotation
which declares

* the direction (<code>IN</code>, <code>OUT</code>, <code>INOUT</code>),
* whether the parameter is required,
* an optional textual description,
* and a label used, e.g. in the graphical user interface automatically generated
to execute the operator.

It is important to add a public standard constructor (without arguments)
to be able to use Java's reflection mechanism.
Finally, the abstract method <code>operate()</code> of <code>ALDOperator</code> has to be overridden
implementing the functionality of the operator.

<pre>
@ALDAOperator(genericExecutionMode=ALDAOperator.ExecutionMode.ALL,
level=ALDAOperator.Level.APPLICATION)
public class MatrixSum extends ALDOperator {

/** Choose row or colum wise sum
*/
public static enum SummarizeMode {
/** row wise */
ROW,

/** column wise */
COLUMN
}

/**
* Input matrix
*/
@Parameter( label= "Input matrix", required = true,
direction = Parameter.Direction.IN, description = "Input matrix.")
private Double[][] matrix;

/**
* Mode of summarizing
*/
@Parameter( label= "Summarize mode", required = true,
direction = Parameter.Direction.IN, description = "Sum over columns or rows?")
private SummarizeMode summarizeMode = SummarizeMode.ROW;

/**
* 1D Array of sums.
*/
@Parameter( label= "sums",
direction = Parameter.Direction.OUT, description = "Row or column wise sums.")
private Double[] sums = null;

/**
* Default constructor.
* @throws ALDOperatorException
*/
public MatrixSum() throws ALDOperatorException {
}

/**
* Constructor.
*
* @param matrix Input matrix.
* @throws ALDOperatorException
*/
public MatrixSum(Double[] [] matrix) throws ALDOperatorException {
this.matrix = matrix;
}

@Override
protected void operate() {
if ( matrix == null )
sums = null;

// calculate sums
if ( summarizeMode == SummarizeMode.ROW ) {
sums = new Double[matrix.length];
for ( int row = 0 ; row < matrix.length ; row++ ) {
sums[row] = 0.0;
for ( int col = 0 ; col < matrix[0].length ; col++ )
sums[row] += matrix[row][col];
}
} else {
sums = new Double[matrix[0].length];
for ( int col = 0 ; col < matrix[0].length ; col++ ) {
sums[col] = 0.0;
for ( int row = 0 ; row < matrix.length ; row++ )
sums[col] += matrix[row][col];
}
}
}
</pre>

These are the basic requirements for the operator to be used on the programming level.
An example of this use is included in the example in the next section.

If we further annotate the class with
<pre>
@ALDAOperator(genericExecutionMode=ALDAOperator.ExecutionMode.ALL)
</pre>
this is all needed to also facilitate
execution of this operator via a graphical and a command line user interface
automatically generated by Alida.
(Setting <code>level=ALDAOperator.Level.APPLICATION</code> declares this operator an application
which is used in the GUI to control display of available operators.)

== Invocation via a graphical user interface ==

Alida comes with one single application to execute Alida operators
with a automatically generated graphical user interface which may be
started from command line by
<pre>
java de.unihalle.informatik.Alida.tools.ALDOpRunnerGUI
</pre>

This will pop up a window to choose an operator to execute.
Arranged according to the package structure all operators allows to be executed
via the graphical user interface according to their <code>genericExecutionMode</code>
are displayed.
Initially packages are unfolded up to a predefined depth.
Unfold the demo package, select <code>MatrixSum</code>, and choose the "Configure Operator" button.
This will pop up another window which allows you to configure the input parameters
of the operator.
Important note: After finishing to input the data matrix entering the final matrix elements
you have to select a previous matrix element due to subtle AWT details.
For the enumeration to select the mode Alida has automatically generated
a combo box to allow convenient selections.
If you are finished with the parameter configuration you want to invoke the operator
using the run button.
On completion of <code>MatrixSum</code> the interface will pop up the result window which allows you
to inspect the outcome of the operation.

== Invocation via command line ==

The command line user interface of Alida allows to invoke all Alida operator
properly annotated to allows generic execution.

You may invoke the matrix summation operator by
<pre>
java de.unihalle.informatik.Alida.tools.ALDOpRunner MatrixSum matrix='[[1,2,3],[4,5,6]]' sums=-
</pre>
which returns as result on standard output
<pre>
sums = [6.0,15.0]
</pre>

Parameter values are specified as name=value pairs.
Alida's syntax for 2D array should be self-explanatory from this example.
As the mode of summation is not supplied as a parameter its default is used

Note, the command
<pre>
java de.unihalle.informatik.Alida.tools.ALDOpRunner MatrixSum matrix='[[1,2,3],[4,5,6]]'
</pre>
will return no output as the command line user interface returns only output parameters requested.

The enumeration defined in <code>MatrixSum</code> is supported by the
user interface without further action required as shown in the next example.
This also demonstrates redirection of output
to a file, sums.out in this case.

<pre>
java de.unihalle.informatik.Alida.tools.ALDOpRunner MatrixSum matrix='[[1,2,3],[4,5,6]]'
summarizeMode=COLUMN sums=@sums.out+
</pre>
Input can be read from file as well:
<pre>
java de.unihalle.informatik.Alida.tools.ALDOpRunner MatrixSum matrix=@data sums=-+
</pre>

where the file data contains the string defining the matrix, e.g., <code>[[1,2,3],[4,5,6]]</code>

= Adding more features to an operator =

We now generalize this example to realize not only summation over rows or
columns, but arbitrary summarizing operations.
This shows Alida's feature to allow an operator as parameter of another operator.

== Implementation ==

First we generalize <code>ALDArraySum</code> to the operator <code>ApplyToMatrix</code>
which also takes a 2D array and an enum indicating the mode of marginalization (<code>ROW</code> or <code>COLUMN</code>).
It takes an additional input parameter which specifies the operation to be applied on each
row or column.

This parameter is itself an Alida operator and of type <code>ALDSummarizeArrayOp</code>
which is implemented as an abstract class.
This abstract operator defines a summarizing operator
which takes a 1D array as input and returns a summarizing scalar.
As this is an abstract class there is no need to override the <code>operate()</code>
method, however some getter and setter methods are provided.

<pre>
@Parameter( label= "Input 1D array", required = true,
direction = Parameter.Direction.IN, description = "Input array (1D).")
protected Double[] data;

/**
* Summarizing scalar
*/
@Parameter( label= "Summarizing scalar",
direction = Parameter.Direction.OUT, description = "Summarizing scalar of the 1D arra")
protected Double summary = null;

/**
* Default constructor.
* @throws ALDOperatorException
*/
public ALDSummarizeArrayOp() throws ALDOperatorException {
}

/**
* Returns the 1D array
* @return data array
*/
public Double[] getData() {
return this.data;
}

/**
* Sets the 1D array
* @param data
*/
public void setData( Double[] data) {
this.data = data;
}

</pre>

Now we add concrete examples of such a summarizing operation, in this case
summation (<code>ALDArraySum</code>), to return the mean (<code>ALDArrayMean</code>), and the minimum (<code>ALDArrayMin</code>).
Each implements the <code>operate()</code> method and has to supply a standard constructor.
In this example we add another constructor for convenience.
This operators are declared as operators on the standard in contrast to
application level, as they are not expected to be invoked as an application.
However, setting the level to standard in the menu of the graphical user interface
stills allows their execution.
When extending the abstract super class it is necessary to annotate the
class with <code>@ALDDerivedClass</code> in order to allow Alida's dataIO mechanism to find the derived class
in the automatically generated user interface.
This holds for other parameter types as well.
More specifically, if an instance of a class is to be supplied in an automatically
generated user interface as a value for a parameter of one of its super classes,
Alida requires the annotation <code>@ALDDerivedClass</code>.

<pre>
@ALDDerivedClass
@ALDAOperator(genericExecutionMode=ALDAOperator.ExecutionMode.ALL,
level=ALDAOperator.Level.STANDARD)
public class ALDArraySum extends ALDSummarizeArrayOp {

@Override
protected void operate() {
summary = 0.0;
for ( int i = 0 ; i < data.length ; i++ )
summary += data[i];
}

/**
* Default constructor.
* @throws ALDOperatorException
*/
public ALDArraySum() throws ALDOperatorException {
}

</pre>

Now we are ready to implement
the <code>ApplyToMatrix</code> operator, which also demonstrates supplemental parameters.
This supplementals, e.g., control debugging output or returning of intermediate results.
For demo purposes we declare a supplemental input parameter <code>returnElapsedTime</code>.
If it is set to true the operator will return the elapsed time in a second
supplemental parameter with direction output.

Again, the operation is implemented in the <code>operate()</code> method and the remainder of the
class supplies getter and setter methods for convenience.
The <code>operate()</code> method give also an example of the invocation of an operator on the
programming level.
In this case, an instance of the operator is already passed as a parameter.
Its parameters are set, in this case each 1D array to be summarized in turn.
Upon return from the method <code>runOp()</code> the results may be retrieved from the operator object,
in this example with the <code>getSummary()</code> method.
Besides getter and setter methods as implemented in each operator
Alida provides also a generic get and set methods applicable to
all parameters of an operator.
Note, that the operator is not invoked by its <code>operate()</code> method, but via
the <code>runOp()</code> method implemented the base class <code>ALDOperator</code>.
This methods validates the parameters before invocation of <code>operate()</code>.
Furthermore, it take all necessary measures for Alida's processing
history which automatically logs
all manipulative actions on the data and corresponding parameter settings.

<pre>
@ALDAOperator(genericExecutionMode=ALDAOperator.ExecutionMode.ALL,
level=ALDAOperator.Level.APPLICATION)
public class ApplyToMatrix extends ALDOperator {

/** Choose row or colum wise sum
*/
public static enum SummarizeMode {
/** row wise */
ROW,
/** column wise */
COLUMN
}

/**
* Input matrix
*/
@Parameter( label= "Input matrix", required = true,
direction = Parameter.Direction.IN, description = "Input matrix.")
private Double[][] matrix;

/**
* Mode of summarizing
*/
@Parameter( label= "Summarize mode", required = true,
direction = Parameter.Direction.IN, description = "Sum over columns or rows.")
private SummarizeMode summarizeMode = SummarizeMode.ROW;

/**
* Summarizing opererator
*/
@Parameter( label= "Summarizing operator", required = true,
direction = Parameter.Direction.IN, description = "Specifies the summarizing operation to apply")
private ALDSummarizeArrayOp summarizeOp;

/**
* 1D Array of summaries.
*/
@Parameter( label= "summaries",
direction = Parameter.Direction.OUT, description = "Row or column wise summaries")
private Double[] summaries = null;

/**
* Supplemental to request elapsed time to be returned
*/
@Parameter( label= "Return elapsed time",
direction = Parameter.Direction.IN, description = "Request elapsed time consumed to be returned",
supplemental=true)
private boolean returnElapsedTime = false;

/**
* Elpased time
*/
@Parameter( label= "Elapsed time",
direction = Parameter.Direction.OUT, description = "Elapsed time of operation in milliseconds",
supplemental=true)
private long elapsedTime;

/**
* Default constructor.
* @throws ALDOperatorException
*/
public ApplyToMatrix() throws ALDOperatorException {
}

/**
* Constructor.
*
* @param matrix Input matrix.
* @throws ALDOperatorException
*/
public ApplyToMatrix(Double[] [] matrix) throws ALDOperatorException {
this.matrix = matrix;
}

@Override
protected void operate() throws ALDOperatorException,ALDProcessingDAGException {
if ( returnElapsedTime )
elapsedTime = System.currentTimeMillis();

if ( matrix == null )
summaries = null;

// calculate summaries
if ( summarizeMode == SummarizeMode.ROW ) {
summaries = new Double[matrix.length];
for ( int row = 0 ; row < matrix.length ; row++ ) {
summarizeOp.setData(matrix[row]);
summarizeOp.runOp();
summaries[row] = summarizeOp.getSummary();
}
} else {
summaries = new Double[matrix[0].length];
Double[] tmp = new Double[matrix.length];
for ( int col = 0 ; col < matrix[0].length ; col++ ) {
for ( int row = 0 ; row < matrix.length ; row++ )
tmp[row] = matrix[row][col];

summarizeOp.setData(tmp);
summarizeOp.runOp();
summaries[col] = summarizeOp.getSummary();
}
}

if ( returnElapsedTime )
elapsedTime = System.currentTimeMillis() - elapsedTime;
}

// ==============================================================
// Getter and setter methods
/** Get value of returnElapsedTime.
* Explanation: Request elapsed time consumed to be returned.
* @return value of returnElapsedTime
*/
public boolean getReturnElapsedTime(){
return returnElapsedTime;
}

/** Set value of returnElapsedTime.
* Explanation: Request elapsed time consumed to be returned.
* @param value New value of returnElapsedTime
*/
public void setReturnElapsedTime( boolean value){
this.returnElapsedTime = value;
}
</pre>

== Invocation via a graphical user interface ==

If the graphical interface is still running just select our new operator
and begin to configure it.
For the parameter summarizing operator you have a choice of all operators extending
the abstract operator <code>ALDSummarizeArrayOp</code>.
All which is necessary on the implementation side is proper annotation of the extending
classes with <code>@ALDDerivedClass</code>.
As the selected operator may have its own parameters you may want to configure it.
In our example this is not necessary as the input array is, of course, supplied
by the <code>ApplyToMatrix</code> operator.
Do not forget to input your data before hitting the run button.
After return, again a result window give you the results of the operation.
Note, if you did not tick Return elapsed time" this window will show zero
for the time elapsed as the operator has not been request to stop the time.

== Invocation via command line ==

When invoking the <code>ApplyToMatrix</code> operator from command line
we have to handle derived classes as value for parameters.
In the graphical user interface Alida features a combo box where
we may choose from.
In the command line interface Alida allows to prefix the value of a parameter
with a derived class to be passed to the operator.
This is necessary as Alida as, of course, no way to itself
decide if and which derived class is to be used.
Alida's syntax is to enclose the class name in a dollar sign and a colon.
As evident in the following example, abbreviations are of the fully
qualified class name are accepted as long as they are unambiguous.
<pre>
java de.unihalle.informatik.Alida.tools.ALDOpRunner Apply \
matrix='[[1,2,3],[4,5,6]]' \
summarizeMode=ROW \
summarizeOp='<math>ALDArrayMean:{}' \
summaries=-
</pre>
results in
<pre>
summaries = [2.0,5.0]
</pre>

<code>ALDOpRunner</code> may be persuaded to show all operators derived from <code>ALDSummarizeArrayOp</code>
and known within the user interface if we enter an invalid class name:
<pre>
java de.unihalle.informatik.Alida.tools.ALDOpRunner \
Apply matrix='[[1,2,3],[4,5,6]]' \
summarizeMode=ROW summarizeOp='</math>dd:{}' \
summaries=-
</pre>
yields
<pre>
ALDStandardizedDataIOCmdline::readData found 0 derived classes matching <dd>
derived classes available:
de.unihalle.informatik.Alida.demo.ALDArrayMean
de.unihalle.informatik.Alida.demo.ALDArrayMin
de.unihalle.informatik.Alida.demo.ALDArraySum
ERROR: reading parameter <summarizeOp> returns null
</pre>

Supplemental parameters are handled like other parameters
<pre>
java de.unihalle.informatik.Alida.tools.ALDOpRunner Apply \
matrix='[[1,2,3],[4,5,6]]' \
summarizeMode=COLUMN \
summarizeOp='<math>ALDArrayMin:{}' \
summaries=- \
returnElapsedTime=true \
elapsedTime=-
</pre>
gives
<pre>
summaries = [1.0,2.0,3.0]
elapsedTime = 4
</pre>

= Adding more data types as parameters =

Alida provides automatic IO of primitive data types, enumerations, arrays, collections,
and operators.
In addition so called parameterized classes are supported.
Any Java class may be declared to be a parameterized class in Alida
by annotating the class <code>@ALDParametrizedClass</code> as shown in the
class <code>ExperimentalData</code>.
All member variables to be known to and handled by Alida's user interface
simply need to be annotated with <code>@ALDClassParameter</code>.

Here we implement a toy version of experimental data <code>ExperimentalData</code>.
A complete experiment consists of a number of independent repetitions of
sub experiments.
In each of these the same features (measurements) are recorded.
The measurements a represented in
a 2D array of Doubles, where each column represents
one sub experiment and the rows the distinct features.
The measurements may be normalized which is indicated by the
normalized member variable.

The class is annotated by <code>@ALDParametrizedClass</code>, and
and all members to be handle in Alida'a user interfaces are
to be annotated with <code>@ALDParametrizedClass</code>.
The label field has the same semantics as for parameters of operators.
These annotations are the only implementational overhead
to allow Alida to automatically generate user interfaces
where the parameterized class acts a a parameter.

<pre>
@ALDParametrizedClass
@ALDMetaInfo(export=ALDMetaInfo.ExportPolicy.MANDATORY)
public class ExperimentalData {
@ALDClassParameter(label="description")
private String description = null;

@ALDClassParameter(label="data")
private Double[][] data = null;

/** are the data normalized
*/
@ALDClassParameter(label="Is normalized")
private boolean normalized = false;

/** Standard constructor is needed
*/
public ExperimentalData() {
}

/** Constructor for an experiment.
* Normalized is assumed to be false.
*
* @param description a textual desciption of the experiment
* @param data measurements
*/
public ExperimentalData( String description, Double[][] data) {
this( description, data, false);
}

/** Constructor for an experiment.
*
* @param description a textual desciption of the experiment
* @param data measurements
* @param normalized are the data normalized
*/
public ExperimentalData( String description, Double[][] data, boolean normalized) {
this.normalized = normalized;
this.description = description;
this.setData( data, normalized);
}
</pre>

This is shown below for a simple normalizing operator <code>NormalizeExperimentalDataOp</code>
which takes experimental data as input an returns a new instance
of <code>ExperimentalData</code> which contains normalized data.

<pre>
@ALDAOperator(genericExecutionMode=ALDAOperator.ExecutionMode.ALL,
level=ALDAOperator.Level.APPLICATION)
public class NormalizeExperimentalDataOp extends ALDOperator {

/**
* Input data
*/
@Parameter( label= "Experimental data", required = true,
direction = Parameter.Direction.IN, description = "Experimental data to be normalized")
private ExperimentalData experiment = null;

/**
* Normalized experiment to be returned
*/
@Parameter( label= "Normalized experiment",
direction = Parameter.Direction.OUT, description = "Normalized experiment")
private ExperimentalData result = null;

/**
* Default constructor.
* @throws ALDOperatorException
*/
public NormalizeExperimentalDataOp() throws ALDOperatorException {
}

/**
* Constructor.
*
* @param experiment Experimental data
* @throws ALDOperatorException
*/
public NormalizeExperimentalDataOp(ExperimentalData experiment) throws ALDOperatorException {
this.experiment = experiment;
}

@Override
protected void operate() throws ALDOperatorException,ALDProcessingDAGException {

ApplyToMatrix normalizeOp = new ApplyToMatrix( experiment.getData());
normalizeOp.setSummarizeMode( ApplyToMatrix.SummarizeMode.ROW);
normalizeOp.setSummarizeOp( new ALDArrayMean());
normalizeOp.runOp();

Double[][] normalizedData = (Double[][])(experiment.getData().clone());
for ( int e = 0; e < experiment.getNumExperiments(); e++ ) {
for ( int f = 0 ; f < experiment.getNumFeatures() ; f++ ) {
normalizedData[f][e] -= normalizeOp.getSummaries()[f];
}
}

result = new ExperimentalData( experiment.getDescription() + " (Normalized)", normalizedData, true);
}
</pre>

This mechanism applies in a recursive fashion, i.e. a parameterized class may
(recursively) contain a member variable which itself is a parametrized class.
Likewise, an operator acting as a parameter of another operator
may in turn have a parameter of type <code>ALDOperator</code>.

== Invocation via a graphical user interface ==

Invoking and configuring <code>NormalizeExperimentalDataOp</code> from the graphical user interface
shows as the only required parameter the experimental data.
This parameterized class can be configured in a separate window
very similar to to configuration of operators.
Likewise the resulting normalized experimental data
may be inspected in their own window.

Obviously this is a toy example, as we would not expect the measurements to
be entered manually, but rather stored and read from file in a specialized format.
This is one of the rare cases where
custom data IO provider need to be implemented, in this
case for <code>ExperimentalData</code>.

== Invocation via command line ==

Again, invocation from command line is provided by Alida in an automatic
way with no further implementational overhead.
The syntax for parameterized classes es a comma separated list of name=value pairs
enclosed in curly brackets where name refers to annotated member variables of
the parameterized class.

<pre>
java de.unihalle.informatik.Alida.tools.ALDOpRunner NormalizeExperimentalDataOp \
experiment='{data=[[1,2,3],[2,2,2],[100,103,110]],description="Demo experiment"}' \
result=-
</pre>
yields
<pre>
result = { normalized = true ,
description = "Demo experiment" (Normalized) ,
data = [[-1.0,0.0,1.0],[0.0,0.0,0.0],
[-4.333333333333329,-1.3333333333333286,5.666666666666671]] }
</pre>

If a class derived from <code>ExperimentalData</code> was to be supplied to the operator,
the curly brackets can be prefixed by a derive class definition starting with a dollar sign
and ending with a colon as shown for the summarizing operators above.

MediaWiki:Sidebar

2012-03-02T11:46:40Z

Sysop:

* navigation
** mainpage|mainpage-description
** Quickstart|Quickstart and Code Examples
** Downloads|Downloads
** Projects|Related Projects and Publications
** Recent_changes|Recent Changes
** Acknowledge|Acknowledgements
** Alida:About|Imprint
* documentation
** features|Features
** http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf|Manual
** code_examples|Code examples
** http://www2.informatik.uni-halle.de/agprbio/alida/api/index.html|Javadoc API
** frequently_asked_questions|FAQs
* development
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php|Bug report
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php|Feature request
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php|Report overview
* SEARCH
* TOOLBOX
* LANGUAGES

Main Page

2012-03-02T08:46:03Z

Sysop: /* News */

== [[News]] ==

Alida release 1.2 has just been published! You can get the new version in the download section!

Main new feature: generic user interface generation for operators to use them from commandline and via a Swing GUI!

== Alida - Advanced Library for Integrated Development of data analysis Applications ==

...formerly known as Alida - Automatic Logging of Process Information in Data Analysis

Alida is a library to support and simplify algorithm development in the field of data analysis. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoced in a predefined way.

Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.

Alida's operator concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commanline interfaces.

== Licensing information ==
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].

== Current release ==
You can download Alida version 1.2 [[Downloads | here]]. 
You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/index.html here]. 
Furthermore Alida offers you a user and programmer manual you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here].

== Bug reports & Feature requests ==
Bug reports and feature requests can be submitted via the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php bugtracking system] or by mail to [mailto:alida@informatik.uni-halle.de alida@informatik.uni-halle.de]. 
Before reporting a new bug, please check if that bug has already been submitted in the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php report list].

MediaWiki:Sidebar

2012-03-02T08:45:19Z

Sysop:

* navigation
** mainpage|mainpage-description
** Quickstart|Quickstart
** Downloads|Downloads
** Projects|Related Projects and Publications
** Recent_changes|Recent Changes
** Acknowledge|Acknowledgements
** Alida:About|Imprint
* documentation
** features|Features
** http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf|Manual
** code_examples|Code examples
** http://www2.informatik.uni-halle.de/agprbio/alida/api/index.html|Javadoc API
** frequently_asked_questions|FAQs
* development
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php|Bug report
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php|Feature request
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php|Report overview
* SEARCH
* TOOLBOX
* LANGUAGES

Quickstart

2012-03-02T08:44:06Z

Sysop: Created page with "To try Alida and learn more about its nice features, do the following: * download the binary zipfile from the download section of this website * unzip its contents to a director..."

To try Alida and learn more about its nice features, do the following:

* download the binary zipfile from the download section of this website
* unzip its contents to a directory of your choice
* download required external Java libraries as mentioned on the download page
* run the graphical operator runner as follows:

java -cp ./Alida.jar:./extjars/sezpoz-1.9-alida.jar:./extjars/jh.jar:./extjars/xstream-1.3.1.jar:./intjars/Alida-Help.jar de.unihalle.informatik.Alida.tools.ALDOpRunnerGUI

* Have fun!

MediaWiki:Sidebar

2012-03-02T08:40:28Z

Sysop:

* navigation
** mainpage|mainpage-description
** Quickstart|Quickstart
** Downloads|Downloads
** Projects|Related Projects and Publications
** Recent_changes|Recent Changes
** Acknowledge|Acknowledgements
** Alida:About|Imprint
* documentation
** features|Features
** http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf|Manual
** http://www2.informatik.uni-halle.de/agprbio/alida/api/index.html|Javadoc API
** frequently_asked_questions|FAQs
** code_examples|Code examples
* development
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php|Bug report
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php|Feature request
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php|Report overview
* SEARCH
* TOOLBOX
* LANGUAGES

Main Page

2012-03-02T08:39:12Z

Sysop: /* Current release */

== [[News]] ==

Alida release 1.2 has just been published! You can get the new version in the download section!

Main new feature: generic user interface generation for commandline and Swing GUI environments!

== Alida - Advanced Library for Integrated Development of data analysis Applications ==

...formerly known as Alida - Automatic Logging of Process Information in Data Analysis

Alida is a library to support and simplify algorithm development in the field of data analysis. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoced in a predefined way.

Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.

Alida's operator concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commanline interfaces.

== Licensing information ==
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].

== Current release ==
You can download Alida version 1.2 [[Downloads | here]]. 
You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/index.html here]. 
Furthermore Alida offers you a user and programmer manual you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here].

== Bug reports & Feature requests ==
Bug reports and feature requests can be submitted via the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php bugtracking system] or by mail to [mailto:alida@informatik.uni-halle.de alida@informatik.uni-halle.de]. 
Before reporting a new bug, please check if that bug has already been submitted in the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php report list].

Main Page

2012-03-02T08:38:51Z

Sysop: /* Current release */

== [[News]] ==

Alida release 1.2 has just been published! You can get the new version in the download section!

Main new feature: generic user interface generation for commandline and Swing GUI environments!

== Alida - Advanced Library for Integrated Development of data analysis Applications ==

...formerly known as Alida - Automatic Logging of Process Information in Data Analysis

Alida is a library to support and simplify algorithm development in the field of data analysis. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoced in a predefined way.

Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.

Alida's operator concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commanline interfaces.

== Licensing information ==
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].

== Current release ==
You can download Alida version 1.2 [[Downloads | here]]. 
You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/index.html here]. 
Furthermore Alida offers you a user and programmer manual you can download [http://www2.informatik.uni-halle.de/agprbio/alida/manual/AlidaManual.pdf here].

== Bug reports & Feature requests ==
Bug reports and feature requests can be submitted via the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php bugtracking system] or by mail to [mailto:alida@informatik.uni-halle.de alida@informatik.uni-halle.de]. 
Before reporting a new bug, please check if that bug has already been submitted in the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php report list].

Alida:About

2012-03-02T08:36:09Z

Sysop:

Alida is a project of the Martin Luther University Halle-Wittenberg. 

'''Editors:''' 
* Stefan Posch
* Birgit Möller 

'''Contact:''' 
* [mailto:alida@informatik.uni-halle.de alida@informatik.uni-halle.de] 

'''Institution:''' 
Institute of Computer Science 
Faculty of Natural Science III 
Martin Luther University Halle-Wittenberg 
Von-Seckendorff-Platz 1, 06120 Halle, Germany

Main Page

2012-03-02T08:34:49Z

Sysop:

== [[News]] ==

Alida release 1.2 has just been published! You can get the new version in the download section!

Main new feature: generic user interface generation for commandline and Swing GUI environments!

== Alida - Advanced Library for Integrated Development of data analysis Applications ==

...formerly known as Alida - Automatic Logging of Process Information in Data Analysis

Alida is a library to support and simplify algorithm development in the field of data analysis. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoced in a predefined way.

Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.

Alida's operator concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commanline interfaces.

== Licensing information ==
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].

== Current release ==
You can download Alida version 1.2 [[Downloads | here]]. 
You can find the API documentation for this release [http://www.informatik.uni-halle.de/alida/api/index.html here]. 
Furthermore Alida offers you a user and programmer manual you can download [http://www.informatik.uni-halle.de/alida/downloads/manual/AlidaManual.pdf here].

== Bug reports & Feature requests ==
Bug reports and feature requests can be submitted via the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php bugtracking system] or by mail to [mailto:alida@informatik.uni-halle.de alida@informatik.uni-halle.de]. 
Before reporting a new bug, please check if that bug has already been submitted in the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php report list].

Downloads

2012-03-02T08:33:14Z

Sysop: /* Requirements */

__NOTOC__
== Requirements ==
Alida requires Java 1.6 or later.

The following external jars are needed to use Alida:

* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
* [http://xstream.codehaus.org/ XStream], Version 1.3.1
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05

In addition, Alida requires some more libraries which are either in-house developments or result from modifications of other libraries:

* We use a slightly modified version of [http://http://sezpoz.java.net/ SezPoz] for annotation indexing. You can get the modified version [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/sezpoz-1.9-alida.jar here].
* Alida also requires some graphml extensions to be found in '''''aldgraphml.jar''''' [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/aldgraphml.jar jar].
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System], the corresponding '''Alida-Help.jar''' can be found [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida-Help.jar here].

If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile. Make sure that all of them are in the classpath when executing the operator runners. 

== Current release (v1.2)==
* Alida Binaries [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin.zip zip] (includes Alida binaries, license information and the file ''aldgraphml.jar'' with Alida's extensions of graphml)
* Alida Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src.zip zip] (includes only the sources, license files and some READMEs on how to use and compile Alida)
* Alida API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api.zip zip] (includes Javadocs of Alida's API)
 

== All versions of Alida ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Binaries
! Sources
! API
! Date
|-
| 1.2
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api-1.2.zip zip]
| March 2nd, 2012
|-
| 1.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api-1.1.zip zip]
| Sep 14th, 2011
|-
| 1.0
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api-1.0.zip zip]
| May 9th, 2011
|}
 

== Manual ==

Detailed information about Alida, its API and usage, can be found in the user and programmer manual.

* Alida-Manual, Version 1.0 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf]
 

== Additional resources ==

* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.
 
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.

* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'. 
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'. 
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.
 
Download the current release:
[http
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]
Source code for Chipory is available upon request.
 

== Logo ==

* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]

Downloads

2012-03-02T08:33:03Z

Sysop: /* Requirements */

__NOTOC__
== Requirements ==
Alida requires Java 1.6 or later.

The following external jars are needed to use Alida:

* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
* [http://xstream.codehaus.org/ XStream], Version 1.3.1
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05

In addition, Alida requires some more libraries which are either in-house developments or result from modifications of other libraries:

* We use a slightly modified version of [http://http://sezpoz.java.net/ SezPoz] for annotation indexing. You can get the modified version [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/sezpoz-1.9-alida.jar here].
* Alida also requires some graphml extensions to be found in '''''aldgraphml.jar''''' [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/aldgraphml.jar jar].
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System], the corresponding '''Alida-Help.jar''' can be found [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida-Help.jar here].

If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile. Make sure that all of them are in the classpath when executing the operator runners. 

== Current release (v1.2)==
* Alida Binaries [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin.zip zip] (includes Alida binaries, license information and the file ''aldgraphml.jar'' with Alida's extensions of graphml)
* Alida Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src.zip zip] (includes only the sources, license files and some READMEs on how to use and compile Alida)
* Alida API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api.zip zip] (includes Javadocs of Alida's API)
 

== All versions of Alida ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Binaries
! Sources
! API
! Date
|-
| 1.2
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api-1.2.zip zip]
| March 2nd, 2012
|-
| 1.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api-1.1.zip zip]
| Sep 14th, 2011
|-
| 1.0
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api-1.0.zip zip]
| May 9th, 2011
|}
 

== Manual ==

Detailed information about Alida, its API and usage, can be found in the user and programmer manual.

* Alida-Manual, Version 1.0 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf]
 

== Additional resources ==

* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.
 
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.

* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'. 
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'. 
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.
 
Download the current release:
[http
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]
Source code for Chipory is available upon request.
 

== Logo ==

* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]

Downloads

2012-03-02T08:31:47Z

Sysop: /* Current release (v1.1) */

__NOTOC__
== Requirements ==
Alida requires Java 1.6 or later.

The following external jars are needed to use Alida:

* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
* [http://xstream.codehaus.org/ XStream], Version 1.3.1
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05

In addition, Alida requires some more libraries which are either in-house developments or result from modifications of other libraries:

* We use a slightly modified version of [http://http://sezpoz.java.net/ SezPoz] for annotation indexing. You can get the modified version [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/sezpoz-1.9-alida.jar here].
* Alida also requires some graphml extensions to be found in '''''aldgraphml.jar''''' [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/aldgraphml.jar jar].
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System], the corresponding '''Alida-Help.jar''' can be found [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida-Help.jar here].

If you download the Alida binary zipfile you will find these two libraries in the subdirectory intjars of the zipfile. 

== Current release (v1.2)==
* Alida Binaries [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin.zip zip] (includes Alida binaries, license information and the file ''aldgraphml.jar'' with Alida's extensions of graphml)
* Alida Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src.zip zip] (includes only the sources, license files and some READMEs on how to use and compile Alida)
* Alida API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api.zip zip] (includes Javadocs of Alida's API)
 

== All versions of Alida ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Binaries
! Sources
! API
! Date
|-
| 1.2
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api-1.2.zip zip]
| March 2nd, 2012
|-
| 1.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api-1.1.zip zip]
| Sep 14th, 2011
|-
| 1.0
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api-1.0.zip zip]
| May 9th, 2011
|}
 

== Manual ==

Detailed information about Alida, its API and usage, can be found in the user and programmer manual.

* Alida-Manual, Version 1.0 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf]
 

== Additional resources ==

* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.
 
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.

* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'. 
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'. 
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.
 
Download the current release:
[http
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]
Source code for Chipory is available upon request.
 

== Logo ==

* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]

Downloads

2012-03-02T08:31:33Z

Sysop: /* All versions of Alida */

__NOTOC__
== Requirements ==
Alida requires Java 1.6 or later.

The following external jars are needed to use Alida:

* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
* [http://xstream.codehaus.org/ XStream], Version 1.3.1
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05

In addition, Alida requires some more libraries which are either in-house developments or result from modifications of other libraries:

* We use a slightly modified version of [http://http://sezpoz.java.net/ SezPoz] for annotation indexing. You can get the modified version [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/sezpoz-1.9-alida.jar here].
* Alida also requires some graphml extensions to be found in '''''aldgraphml.jar''''' [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/aldgraphml.jar jar].
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System], the corresponding '''Alida-Help.jar''' can be found [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida-Help.jar here].

If you download the Alida binary zipfile you will find these two libraries in the subdirectory intjars of the zipfile. 

== Current release (v1.1)==
* Alida Binaries [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin.zip zip] (includes Alida binaries, license information and the file ''aldgraphml.jar'' with Alida's extensions of graphml)
* Alida Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src.zip zip] (includes only the sources, license files and some READMEs on how to use and compile Alida)
* Alida API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api.zip zip] (includes Javadocs of Alida's API)
 

== All versions of Alida ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Binaries
! Sources
! API
! Date
|-
| 1.2
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api-1.2.zip zip]
| March 2nd, 2012
|-
| 1.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api-1.1.zip zip]
| Sep 14th, 2011
|-
| 1.0
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api-1.0.zip zip]
| May 9th, 2011
|}
 

== Manual ==

Detailed information about Alida, its API and usage, can be found in the user and programmer manual.

* Alida-Manual, Version 1.0 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf]
 

== Additional resources ==

* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.
 
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.

* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'. 
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'. 
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.
 
Download the current release:
[http
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]
Source code for Chipory is available upon request.
 

== Logo ==

* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]

Downloads

2012-03-02T08:31:00Z

Sysop: /* Requirements */

__NOTOC__
== Requirements ==
Alida requires Java 1.6 or later.

The following external jars are needed to use Alida:

* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
* [http://xstream.codehaus.org/ XStream], Version 1.3.1
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05

In addition, Alida requires some more libraries which are either in-house developments or result from modifications of other libraries:

* We use a slightly modified version of [http://http://sezpoz.java.net/ SezPoz] for annotation indexing. You can get the modified version [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/sezpoz-1.9-alida.jar here].
* Alida also requires some graphml extensions to be found in '''''aldgraphml.jar''''' [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/aldgraphml.jar jar].
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System], the corresponding '''Alida-Help.jar''' can be found [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida-Help.jar here].

If you download the Alida binary zipfile you will find these two libraries in the subdirectory intjars of the zipfile. 

== Current release (v1.1)==
* Alida Binaries [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin.zip zip] (includes Alida binaries, license information and the file ''aldgraphml.jar'' with Alida's extensions of graphml)
* Alida Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src.zip zip] (includes only the sources, license files and some READMEs on how to use and compile Alida)
* Alida API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api.zip zip] (includes Javadocs of Alida's API)
 

== All versions of Alida ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Binaries
! Sources
! API
! Date
|-
| 1.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api-1.1.zip zip]
| Sep 14th, 2011
|-
| 1.0
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api-1.0.zip zip]
| May 9th, 2011
|}
 

== Manual ==

Detailed information about Alida, its API and usage, can be found in the user and programmer manual.

* Alida-Manual, Version 1.0 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf]
 

== Additional resources ==

* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.
 
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.

* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'. 
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'. 
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.
 
Download the current release:
[http
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]
Source code for Chipory is available upon request.
 

== Logo ==

* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]

Downloads

2012-03-02T08:21:41Z

Sysop: /* Requirements */

__NOTOC__
== Requirements ==
Alida requires Java 1.6 or later.

The following external jars are needed to use Alida:

* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
* [http://xstream.codehaus.org/ XStream], Version 1.3.1

In addition, Alida requires some more libraries which are either in-house developments or result from modifications of other libraries:

* we use a slightly modified version of [http://http://sezpoz.java.net/ SezPoz] for annotation indexing. You can get the modified version [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/sezpoz-1.9-alida.jar here].
* Alida also requires some graphml extensions to be found in '''''aldgraphml.jar''''' [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/aldgraphml.jar jar]. 

If you download the Alida binary zipfile you will find these two libraries in the subdirectory intjars of the zipfile. 

== Current release (v1.1)==
* Alida Binaries [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin.zip zip] (includes Alida binaries, license information and the file ''aldgraphml.jar'' with Alida's extensions of graphml)
* Alida Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src.zip zip] (includes only the sources, license files and some READMEs on how to use and compile Alida)
* Alida API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api.zip zip] (includes Javadocs of Alida's API)
 

== All versions of Alida ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Binaries
! Sources
! API
! Date
|-
| 1.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api-1.1.zip zip]
| Sep 14th, 2011
|-
| 1.0
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api-1.0.zip zip]
| May 9th, 2011
|}
 

== Manual ==

Detailed information about Alida, its API and usage, can be found in the user and programmer manual.

* Alida-Manual, Version 1.0 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf]
 

== Additional resources ==

* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.
 
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.

* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'. 
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'. 
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.
 
Download the current release:
[http
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]
Source code for Chipory is available upon request.
 

== Logo ==

* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]

Main Page

2012-03-01T17:21:45Z

Sysop:

== Note: the new release of Alida will be available for download very soon! ==

== Alida - Advanced Library for Integrated Development of data analysis Applications ==

...formerly known as Alida - Automatic Logging of Process Information in Data Analysis

Alida is a library to support and simplify algorithm development in the field of data analysis. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoced in a predefined way.

Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.

Alida's operator concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commanline interfaces.

== [[News]] ==

Alida release 1.2 has just been published! You can get the new version in the download section soon...

== Licensing information ==
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].

== Current release ==
You can download Alida version 1.1 [[Downloads | here]]. 
You can find the API documentation for this release [http://www.informatik.uni-halle.de/alida/api/index.html here]. 
Furthermore Alida offers you a user and programmer manual you can download [http://www.informatik.uni-halle.de/alida/downloads/manual/AlidaManual.pdf here].

== Bug reports & Feature requests ==
Bug reports and feature requests can be submitted via the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php bugtracking system] or by mail to [mailto:alida@informatik.uni-halle.de alida@informatik.uni-halle.de]. 
Before reporting a new bug, please check if that bug has already been submitted in the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php report list].

Main Page

2012-03-01T17:10:57Z

Sysop: /* News */

== Alida - Advanced Library for Integrated Development of data analysis Applications ==

...formerly known as Alida - Automatic Logging of Process Information in Data Analysis

Alida is a library to support and simplify algorithm development in the field of data analysis. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoced in a predefined way.

Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.

Alida's operator concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commanline interfaces.

== [[News]] ==

Alida release 1.2 has just been published! You can get the new version in the download section soon...

== Licensing information ==
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].

== Current release ==
You can download Alida version 1.1 [[Downloads | here]]. 
You can find the API documentation for this release [http://www.informatik.uni-halle.de/alida/api/index.html here]. 
Furthermore Alida offers you a user and programmer manual you can download [http://www.informatik.uni-halle.de/alida/downloads/manual/AlidaManual.pdf here].

== Bug reports & Feature requests ==
Bug reports and feature requests can be submitted via the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php bugtracking system] or by mail to [mailto:alida@informatik.uni-halle.de alida@informatik.uni-halle.de]. 
Before reporting a new bug, please check if that bug has already been submitted in the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php report list].

Features

2012-03-01T16:41:30Z

Sysop:

__NOTOC__
Alida provides a framework for easy development and usage of data analysis procedures. 

'''Operators''' 
The operator concept is the main ingredient of Alida. It defines a common interface for all operators by which their input and output parameters can be accessed, and which also defines a standardized operator invocation procedure. Moreover, different processing steps of an analysis procedure, i.e. different operator calls, can be linked to a directed graph structure, which allows '''self-documentation''' of the entire analysis process. 
Each resulting data object in Alida, being the result of a certain operator or sequence of operations, is associated with a '''history graph''' in XML format documenting its origins and manipulative actions having been performed on it. 

'''User Interfaces''' 
The clearly defined operator interface and the unified invocation mechanism allows for generic execution of operators based on Alida. 
In particular, generic user interfaces, like GUIs or commandline interfaces, can be generated in a fully automatic way and are well-suited for interaction with arbitrary operators. Alida already includes user interfaces for graphical interaction based on Swing and for executing operators from commandline. 

'''History Graphs''' 
Analysis procedures inherently define an acyclic directed graph data structure which Alida make explicit in terms of 
history graphs. They define visual representations of data analysis procedures subsuming operators, their order of 
invocation and their parameters. The graphs allow for easy archival and later reconstruction of analysis procedure and 
can be visualized in a comfortable manor with '''Chipory'''. 

'''Chipory''' 
Chipory is a comfortable graph visualization tool for exploring graph data structures. It is based on [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio], however, 
extended to meet the special requirements of Alida's history graphs.

MediaWiki:Sidebar

2012-03-01T15:30:14Z

Sysop:

* navigation
** mainpage|mainpage-description
** Downloads|Downloads
** Projects|Related Projects and Publications
** Recent_changes|Recent Changes
** Acknowledge|Acknowledgements
** Alida:About|Imprint
* documentation
** features|Features
** http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf|Manual
** http://www2.informatik.uni-halle.de/agprbio/alida/api/index.html|Javadoc API
** frequently_asked_questions|FAQs
** code_examples|Code examples
* development
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php|Bug report
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php|Feature request
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php|Report overview
* SEARCH
* TOOLBOX
* LANGUAGES

Projects

2012-03-01T15:29:08Z

Sysop: Created page with "== Related Projects == * '''''MiToBo - A microscope image analysis toolbox''''' Webpage: [http://www.informatik.uni-halle.de/mitobo http://www.informatik.uni-halle.de/mitobo]..."

== Related Projects ==

* '''''MiToBo - A microscope image analysis toolbox''''' Webpage: [http://www.informatik.uni-halle.de/mitobo http://www.informatik.uni-halle.de/mitobo]

== Publications ==

* B. Möller, O. Greß and S. Posch, '''''Knowing what happened - Automatic Documentation of Image Analysis Processes''''', In Proc. of 8th International Conference on Computer Vision Systems (ICVS '11), J.L. Crowley, B.A. Draper, and M. Thonnat (Eds.), Springer, LNCS 6962, pp. 1-10. Inria Sophia Antipolis, France, September 2011.

Main Page

2012-03-01T15:24:05Z

Sysop:

== Alida - Advanced Library for Integrated Development of data analysis Applications ==

...formerly known as Alida - Automatic Logging of Process Information in Data Analysis

Alida is a library to support and simplify algorithm development in the field of data analysis. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoced in a predefined way.

Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.

Alida's operator concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commanline interfaces.

== [[News]] ==

Alida release 1.1 has just been published. You can get the new version in the download section.

== Licensing information ==
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].

== Current release ==
You can download Alida version 1.1 [[Downloads | here]]. 
You can find the API documentation for this release [http://www.informatik.uni-halle.de/alida/api/index.html here]. 
Furthermore Alida offers you a user and programmer manual you can download [http://www.informatik.uni-halle.de/alida/downloads/manual/AlidaManual.pdf here].

== Bug reports & Feature requests ==
Bug reports and feature requests can be submitted via the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php bugtracking system] or by mail to [mailto:alida@informatik.uni-halle.de alida@informatik.uni-halle.de]. 
Before reporting a new bug, please check if that bug has already been submitted in the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php report list].

MediaWiki:Sidebar

2012-03-01T15:23:31Z

Sysop:

* navigation
** mainpage|mainpage-description
** Downloads|Downloads
** Projects|Publications and Projects
** Recent_changes|Recent Changes
** Acknowledge|Acknowledgements
** Alida:About|Imprint
* documentation
** features|Features
** http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf|Manual
** http://www2.informatik.uni-halle.de/agprbio/alida/api/index.html|Javadoc API
** frequently_asked_questions|FAQs
** code_examples|Code examples
* development
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php|Bug report
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php|Feature request
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php|Report overview
* SEARCH
* TOOLBOX
* LANGUAGES

Main Page

2012-03-01T15:20:59Z

Sysop: /* Alida - Automatic Logging of Process Information in Data Analysis */

== Alida - Advanced Library for Integrated Development of data analysis Applications ==

...formerly known as Alida - Automatic Logging of Process Information in Data Analysis

Alida is a library to support and simplify algorithm development in the field of data analysis. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoced in a predefined way.

Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.

Alida's operator concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commanline interfaces.

== [[News]] ==

Alida release 1.1 has just been published. You can get the new version in the download section.

----

The concept of Alida will be presented at the 

International Conference on Computer Vision Systems (ICVS '11) 

taking place at Inria Sophia Antipolis, France, in September 2011. 
The title of our talk will be "Knowing what happened - Automatic Documentation of Image Analysis Processes".

== Licensing information ==
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].

== Current release ==
You can download Alida version 1.1 [[Downloads | here]]. 
You can find the API documentation for this release [http://www.informatik.uni-halle.de/alida/api/index.html here]. 
Furthermore Alida offers you a user and programmer manual you can download [http://www.informatik.uni-halle.de/alida/downloads/manual/AlidaManual.pdf here].

== Bug reports & Feature requests ==
Bug reports and feature requests can be submitted via the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php bugtracking system] or by mail to [mailto:alida@informatik.uni-halle.de alida@informatik.uni-halle.de]. 
Before reporting a new bug, please check if that bug has already been submitted in the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php report list].

Frequently asked questions

2011-04-27T07:52:34Z

Sysop: Created page with "__NOTOC__ ...coming soon"

__NOTOC__
...coming soon

Features

2011-04-27T07:50:34Z

Sysop:

__NOTOC__
Alida provides a framework for automatic documentation of data analysis procedures. 

'''Operators''' 
The operator concept is the main ingredient of Alida. By developing such operators, the processing steps 
of an analysis procedure can be linked to a directed graph structure, which allows '''self-documentation''' 
of the entire analysis process. Each resulting data object, being the result of a certain operator or sequence 
of operations, is associated with a '''history graph''' in XML format. 

'''History Graphs''' 
Analysis procedures inherently define an acyclic directed graph data structure which Alida make explicit in terms of 
history graphs. They define visual representations of data analysis procedures subsuming operators, their order of 
invocation and their parameters. The graphs allow for easy archival and later reconstruction of analysis procedure and 
can be visualized in a comfortable manor with '''Chipory'''. 

'''Chipory''' 
Chipory is a comfortable graph visualization tool for exploring graph data structures. It is based on [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio], however, 
extended to meet the special requirements of Alida's history graphs.

Features

2011-04-27T07:44:15Z

Sysop:

Features

2011-04-27T07:42:21Z

Sysop: Created page with "__NOTOC__ The Microscope Image Analysis Toolbox MiToBo contains a lot of new features for scientist, who want to develop new plugins and algorithms in the field of custom im..."

__NOTOC__
The Microscope Image Analysis Toolbox MiToBo contains a lot of new features for scientist, who want to develop 
new plugins and algorithms in the field of custom image analysis and processing, and those who want to use 
custom plugins from [http://rsbweb.nih.gov/ij/ ImageJ] in their daily research. 

A list of contained features and their description in short detail can be found below. 

'''Operators''' 
The operator concept is one of the major features in MiToBo. By developing such operators, the processing steps 
can be linked to a directed graph structure, which allows '''self-documentation''' of the entire image analysis process. 
Each resulting data object, being the result of a certain operator or sequence of operations, is associated with a 
'''history graph''' in XML format. 

'''Plugins''' 
The well known and very powerful plugin concept of [http://rsbweb.nih.gov/ij/ ImageJ] is also available in MiToBo. 
Every user and developer, using MiTobo, can easily create new plugins and customize existing [http://rsbweb.nih.gov/ij/plugins/index.html ImageJ plugins], 
to use the automatic documentation of the plugin via the operator concept of MiToBo for instance. 

'''Data types''' 
MiToBo defines a set of its own data types. For example, a new image data type was developed to improve the 
[http://rsbweb.nih.gov/ij/ ImageJ] image classes. 

'''Applications''' 
Using the plugin and operator concept combined with the large amount of already implemented datatypes and operators, 
a huge coupple of applications on biological and biomedical images can be developed.

Acknowledge

2011-04-27T07:41:31Z

Sysop: Created page with "__NOTOC__ * We thank the [http://www.eclipse.org Eclipse Foundation] for developing the Eclipse IDE, which greatly accelerates the development of Alida. * Many thanks..."

__NOTOC__

* We thank the [http://www.eclipse.org Eclipse Foundation] for developing the Eclipse IDE, which greatly accelerates the development of Alida. 

* Many thanks to Oliver Greß, Danny Misiak and Markus Glaß for fruitful discussions and extensive testing of the framework.

== Contributors ==
* Stefan Posch
* Birgit Möller

MediaWiki:Sidebar

2011-04-27T07:40:04Z

Sysop:

* navigation
** mainpage|mainpage-description
** Downloads|Downloads
** Recent_changes|Recent Changes
** Acknowledge|Acknowledgements
** Alida:About|Imprint
* documentation
** features|Features
** http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual-0.9.pdf|Manual
** http://www.informatik.uni-halle.de/mitobo/api/index.html|Javadoc API
** frequently_asked_questions|FAQs
** code_examples|Code examples
* development
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php|Bug report
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php|Feature request
** http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php|Report overview
* SEARCH
* TOOLBOX
* LANGUAGES