RuntimeMethods

##Creating analysis methods using the graphical user interface

Starting with version 4.0.0, it is possible to create a method at runtime without doing any additional programming, by using the graphical user interface. This is handled using the "Set up parameters" option (see Using ImageAnalysisTools for more information on the interface for this option).

###Enabling method creation

To enable the creation of a method through the user interface, add the parameter labeled "Use created method" from the available parameters. This will override any other method selection either from the parameters file or from the selection in the "Process images in batch" dialog box.

It is also possible to create and run the method without adding this parameter by selecting the method as "DynamicMethod" using the parameter labeled "Name of the method to run" or by selecting "DynamicMethod" from the "Process images in batch" dialog box.

###Setting up the method

This manner of building methods allows creation of simple methods consisting of a string of filters applied in series, followed by a metric to quantify the images.

To string together filters, use the parameter labeled "Add filter...". When this parameter is added to the in-use list, a dialog will pop up showing all known filters. Click on a filter to add that specific filter. Once added, a filter will appear by name in the in-use parameters list. As many filters as desired can be added, and these will be applied in the order they appeared. The filters can be arranged or removed as with any other parameter using the up, down, and remove buttons.

For information on what the filters do, consult the documentation on each filter that can be found in the javadoc repository. In a future version, some basic information about each filter will be incorporated into the user interface.

To select a metric for quantification, use the parameter labeled "Select metric..." which will cause a dialog to appear containing all known metrics. If you don't wish to quantify, select the ZeroMetric, which will just write a zero value (but some metric must be added for the method to work). Only add this parameter a single time.

Add any other parameters that your analysis may require using the interface the same way as you would when not creating a method using the GUI.

When the method is ready, click the done button to write an xml file to disk that specifies the methods and any other parameters that may be required. This will be written to the location specified in the parameter file box in the upper right corner of the window. If a directory is specified, it will be written to the file default.xml in that directory. Any existing file will be overwritten without prompting. If you use the browse button and select an existing file, any work you have done will be replaced by the contents of that file, so select a file first if you want to replace an existing one.

###Running the method

Run the method as you would any existing method by selecting the xml file that was created as your parameters file.

The output generated will be the same as for any other method, and where the method name is appended to output files, it will be called "DynamicMethod".

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