【JIPipe】 【Update IJ package usecase】

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• Intro: https://imagej.net/plugins/jipipe
• Code: https://github.com/applied-systems-biology/jipipe
• How did JIPipe overcome the problems of compatibility?

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• In JIPipe's first installation, it has an automatic dependency check

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• By searching BlackToWhiteTrackBackground in JIPipe project

• We found that the algorithms are registered in ImageAlgorithmsExtension.java,which locates inE:\jipipe\jipipe-ij-algorithms\src\main\java\org\hkijena\jipipe\extensions\imagejalgorithms\ImageJAlgorithmsExtension.java

• for example:

  private void registerThresholdAlgorithms() {
      registerNodeType("ij1-threshold-manual2d-color-hsb", ManualHSBThreshold2DAlgorithm.class, UIUtils.getIconURLFromResources("actions/segment.png"));
      registerNodeType("ij1-threshold-manual2d-color-rgb", ManualRGBThreshold2DAlgorithm.class, UIUtils.getIconURLFromResources("actions/segment.png"));
  ...

  ---

• At the bottom of this file, we have a method:

  
  @Override
  public String getDependencyId() {
      return "org.hkijena.jipipe:imagej-algorithms";
  }

}

- By searching this method `getDependencyId`
- 
![image](https://github.com/Max-ChenFei/VPE_IP/assets/8528052/818b45ae-ebd7-4197-be2f-e4f28c51219e)
- we found this method is used in various situation:
- In `JIPipe.java`:
- We have the Valid Extension check and log error information  

            // Validate ID
            if (!isValidExtensionId(extension.getDependencyId())) {
                System.err.println("Invalid extension ID: " + extension.getDependencyId() + ". Please contact the developer of the extension " + extension);
                progressInfo.log("Invalid extension ID: " + extension.getDependencyId() + ". Please contact the developer of the extension " + extension);
            } else {
                if (!allJavaExtensionsByID.containsKey(extension.getDependencyId())) {
                    allJavaExtensionsByID.put(extension.getDependencyId(), extension);
                } else {
                    System.err.println("Duplicate extension ID: " + extension.getDependencyId() + ". Please contact the developer of the extension " + extension + " or check your ImageJ folder");
                    progressInfo.log("Duplicate extension ID: " + extension.getDependencyId() + ". Please contact the developer of the extension " + extension + " or check your ImageJ folder");
                }
            }

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- This is a part in class `initialize`, and I think it's the dependency check of JIPipe when we first install it

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• By searching System.err.println
• We can find the different error messages JIPipe provide for different situation:

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• We also have logService.warn("Unable to read " + dbPath); to show information about exceptions
• And progress state msg progressInfo.log("No ImageJ update site check is applied.");

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How JIPipe supports ImageJ plugin:

• At first glance, just as we thought earlier, JIPipe only takes the imageJ plugins that has standard input and output:

• which is ImageJ1's marco as they show in the papers' picture:

• 

---

• Also they support IJ2 Ops which also have standard input and output

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JIPipe: Import an image:

reference

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JIPipe: Gaussian filter

• change parameters of the plugin

• the output image can also be displayed with ImageJ UI

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JIPipe threshold segmentation

• The different threshold segmentation method could be chosen from Parameter:

• sementation result:
• Refenrence

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---

After going through the tutorial of JIPipe and comparing with source code,

• I have the following findings:

• 1. dependency check for weka segmentation

• 2. ImageJ1 marco:

• 

• 3. ImageJ2 Ops auto node:

• 

• 4. Further GUI and code for complex plugins such as weka segmentation:

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Conclusion: Just as we predicted, JIPipe only support the plugins that already fit our guideline, which is the ImageJ1 Marco and ImageJ2 Op that has standard input and output interface.

• Our guidelines are for those who would like to use a customized plugin and don't know how to fit the standard