
package de.ipk.ag_ba.plugins.pipelines.maize;



import iap.blocks.acquisition.BlCreateDummyReferenceIfNeeded;

import iap.blocks.acquisition.BlLoadImages;

import iap.blocks.data_structures.ImageAnalysisBlock;

import iap.blocks.extraction.BlCalcAreas;

import iap.blocks.extraction.BlCalcColorHistograms;

import iap.blocks.extraction.BlCalcConvexHull;

import iap.blocks.extraction.BlCalcMainAxis;

import iap.blocks.extraction.BlCalcVolumes;

import iap.blocks.extraction.BlCalcWidthAndHeight;

import iap.blocks.extraction.BlSkeletonizeNir;

import iap.blocks.extraction.BlSkeletonizeVisFluo;

import iap.blocks.postprocessing.BlDrawSkeleton;

import iap.blocks.postprocessing.BlHighlightNullResults;

import iap.blocks.postprocessing.BlMoveMasksToImageSet;

import iap.blocks.postprocessing.BlRunPostProcessors;

import iap.blocks.preprocessing.BlAlign;

import iap.blocks.preprocessing.BlColorBalanceVerticalFluo;

import iap.blocks.preprocessing.BlColorBalanceVerticalNir;

import iap.blocks.preprocessing.BlColorBalanceVerticalVis;

import iap.blocks.preprocessing.BlDetectBlueMarkers;

import iap.blocks.preprocessing.BlRotate;

import iap.blocks.preprocessing.BlCutFromSide;

import iap.blocks.segmentation.BlAdaptiveThresholdNir;

import iap.blocks.segmentation.BlClosing;

import iap.blocks.segmentation.BlIntensityCalculationFluo;

import iap.blocks.segmentation.BlLabFilter;

import iap.blocks.segmentation.BlMedianFilterFluo;

import iap.blocks.segmentation.BlRemoveBackground;

import iap.blocks.segmentation.BlRemoveSmallObjectsVisFluo;

import iap.blocks.segmentation.BlUseFluoMaskToClearOther;

import iap.blocks.unused.BlColorBalanceCircularVisNir;

import de.ipk.ag_ba.plugins.pipelines.AnalysisPipelineTemplate;



/**

 * Analysis workflow for analyzing maize plant images.

 * (V1: tested)

 * 

 * @author Christian Klukas

 */

public class MaizePipeline implements AnalysisPipelineTemplate {

  

  @Override

  public String getTitle() {

    return "Maize Analysis";

  }

  

  @Override

  public String getDescription() {

    return "Analyze Maize Phenotype";

  }

  

  @Override

  public ImageAnalysisBlock[] getBlockList() {

    return new ImageAnalysisBlock[] {

        // acquisition

        new BlLoadImages(),

        new BlCreateDummyReferenceIfNeeded(),

        

        // preprocessing

        new BlRotate(),

        new BlAlign(),

        new BlColorBalanceVerticalVis(),

        new BlColorBalanceVerticalFluo(),

        new BlColorBalanceVerticalNir(),

        new BlColorBalanceCircularVisNir(),

        new BlDetectBlueMarkers(),

        new BlCutFromSide(),

        

        // segmentation

        new BlRemoveBackground(),

        new BlIntensityCalculationFluo(),

        new BlLabFilter(),

        new BlAdaptiveThresholdNir(),

        new BlClosing(),

        new BlMedianFilterFluo(),

        new BlRemoveSmallObjectsVisFluo(),

        new BlUseFluoMaskToClearOther(),

        

        // feature extraction

        new BlSkeletonizeVisFluo(),

        new BlSkeletonizeNir(),

        new BlCalcWidthAndHeight(),

        new BlCalcMainAxis(),

        new BlCalcColorHistograms(),

        new BlCalcConvexHull(),

        new BlCalcAreas(),

        new BlCalcVolumes(),

        

        // postprocessing

        new BlRunPostProcessors(),

        new BlDrawSkeleton(),

        new BlMoveMasksToImageSet(),

        new BlHighlightNullResults()

    };

  }

  

  @Override

  public boolean analyzeTopImages() {

    return true;

  }

  

  @Override

  public boolean analyzeSideImages() {

    return true;

  }

}