Short Description
Simplify the 1D feature extraction task by exposing a simple feature extraction interface.Documentation
Basic Usage
1. Select your sequence as input;
2. Select the axis which you want to extract features on that axis;
3. Select the Extraction Function you want to use, you can choose one from a list of Extraction Functions. Note: the list can be extended by developing a plugin which extended from "featureExtractionPlugin" class.
Feature Extraction Functions have their own options, you can read it on their own documentation.
4. Select concat mode, this is used in case the extraction function will return a multi-channel image, you can choose a method to merge your multi-channel data.
Protocols
Every Feature Extraction function can be used in protocol, you can just search the name of the feature extraction name in protocols.
For example, you can build a plugin with "Sequence extractor" -> "EvaFE In Python" -> "Line Chart Display".
Developing your own feature extraction function
Developing Feature Extraction Function Plugin is extreamly easy.
Setup your developing environment according to:
https://icy.bioimageanalysis.org/index.php?display=startDevWithIcy
New a "Icy Plugin" project with basic template.
Change your project properties, you need to add the following external jar files in your "Java Build Path->Libraries":
1. ICY_HOME/icy.jar
2. ICY_HOME/plugins/adufour/blocks/Blocks.jar
3. ICY_HOME/plugins/adufour/ezplug/EzPlug.jar
4. ICY_HOME/plugins/oeway/featureExtraction/FeatureExtractionEngine.jar
Copy the following template to your class file, and change the package name and class name according to your own settings:
package plugins.tutorial.FEPluginTutorial;
import plugins.oeway.featureExtraction.featureExtractionPlugin;
public class FEPluginTutorial extends featureExtractionPlugin {
@Override
public double[] process(double[] input, double[] position) {
return input;
}
}
The "input" is a array of data extracted from the current image, it depended on the input sequence and the axis you chose to extract. For example, if you want to write a plugin to calculate the "Mean Z-projection" of the input sequence. Your just need to write the following "process" function:
@Override
public double[] process(double[] input, double[] position) {
double[] output = new double[]{ ArrayMath.mean(input)};
return output;
}
Don't forget to "import icy.math.ArrayMath;" to make the mean() function work.
Build a plugin with options GUI
In order to add your own options in GUI, you need to add the following initialization function in your class, and you can add any Ezcomponent or Var<?> to the "optionUI":
EzVarBoolean optionBool = new EzVarBoolean("hello world", false);
@Override
public void initialize(HashMap<String,Object> options,ArrayList
optionUI.add(optionBool);
}
Then you can use the option variable in your process function.
A complete example is like this:
package plugins.tutorial.FEPluginTutorial;
import icy.math.ArrayMath;
import java.util.ArrayList;
import java.util.HashMap;
import plugins.adufour.ezplug.EzVarBoolean;
import plugins.oeway.featureExtraction.featureExtractionPlugin;
public class FEPluginTutorial extends featureExtractionPlugin {
EzVarBoolean optionBool = new EzVarBoolean("calculate mean", false);
@Override
public void initialize(HashMap<String,Object> options,ArrayList
optionUI.add(optionBool);
}
@Override
public double[] process(double[] input, double[] position) {
if(optionBool.getValue())
return input;
else
{
double[] output = new double[]{ ArrayMath.mean(input)};
return output;
}
}
}
A more detailed tutorial on using EzPlug varialbes can be refered here:
https://icy.bioimageanalysis.org/plugin/EzPlug_Tutorial
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