Scripting in QuPath is very essential.
An opportunity to debug QuPath scripts at runtime would be a big advantage.
Here I would like to share and discuss the following approach to debug QuPath scripts in an Eclipse environment.
It delivers the great advantage to use breakpoints inside QuPath scripts, to execute the script code line-wise (Step over, Step into) and to access the content of objects during script execution.
The approach requires:
- QuPath project in Eclipse
- Modification of qupath.lib.gui.scripting.DefaultScriptEditor.java
- Eclipse Groovy Development Tools installed in Eclipse
- QuPath script in Groovy project
(see Setup Details below)
Note:
This approach is currently a first and minimum version. Probably not all options are fully exhausted yet and not all problems are fixed.
The core of the approach is to evaluate the script code directly from the script file with a GroovyShell instead of utilizing the ScriptEngine (as QuPath currently does).
This is necessary to link the script to the debugger.
Therefore I have implemented an additional function in the QuPath ScriptEditor in the menu Run:
- Run Debug (experimental)
The modified version of the DefaultScriptEditor.java is attached here :DefaultScriptEditor.zip (18.5 KB) My changes are marked in the code.
Setup Details
Script file in Eclipse Groovy Project
- Create a Groovy project for the QuPath scripts (my name: qp_scripts)
- Configure the script project settings:
– Groovy Project>Properties>Java Build Path>Projects> Add all qupath projects to the build path (this is used for code auto completion)
– Groovy Project>Properties>Java Build Path>Libraries> If necessary, add other jars to the build path, e.g. gson-2.8.6.jar (this is used for code auto completion)
– Groovy Project>Properties>Groovy Compiler>Enable script folder support = true
**/*.groovy inserted AND selected in pattern list (see image below)
QuPath Project in Eclipse
- Use the modified DefaultScriptEditor.java in the QuPath project. (groovy-3.03.jar, groovy-jsr223-3.03.jar and groovy-xml-3.03.jar have to be added to the class path of the qupath-gui-fx project)
- Configure the QuPath project settings:
– Project>Properties>Run/Debug Settings>QuPath (Launch configuration)>Edit>Source>Add>Workspace Folder> qp_scripts\bin (Class folder of the groovy script project)
– Project>Properties>Project References> Select the Groovy Script project (to build the script project when starting QuPath from Eclipse)
Groovy Project>Properties>Groovy Compiler>Enable script folder support
Usage
- Create a new groovy class file in the source folder of your script project (Right click to src folder>New>Other>Groovy>Groovy Type). The new groovy file MUST be located in the default package!
- Type a simple test script, e.g.
import qupath.lib.scripting.QP
import qupath.lib.projects.Project
import qupath.lib.projects.ProjectImageEntry
print '***** INFO ********\n'
print '*** QuPath Script Debugging Test ***\n'
print 'QuPath script created AND build(!) in Eclipse Groovy project\n'
print 'Debug breakpoints defined in the script\n'
print 'Start QuPath from Eclipse in Debug mode\n'
print 'Open Project in QuPath\n'
print 'Open ScriptEditor and open script file\n'
print 'Run script with function *Run Debug*\n'
print 'Code execution is stopped at script breakpoint\n'
print 'Object content is accessible in the script code\n'
print '***** INFO END ********\n'
def Project project = QP.getProject()
if (project != null) {
for (entry1 in project.getImageList()) {
def name1 = entry1.getImageName()
print name1 +'\n'
}
}
- Save and build the script file (During the build process the script file should have been copied as uncompiled groovy file (AsIs) to the script project class folder, in my case: qp_scripts\bin !)
- Set some debug breakpoints inside the script code
- Start QuPath from Eclipse in Debug mode
- Open the ScriptEditor and load the script file from qp_scripts\src
- Run script in QuPath in Debug mode with new function Run>Run Debug (experimental)
The code execution should be halted at the breakpoint inside the script and you should be able to use the Eclipse debug functions (see first image in this post).
I hope I have not forgotten important setup steps.
Pls reply with questions, problems or feedback.
Limitations
There is always a price.
- In QuPath important default libs are automatically added to the scripts when they are started with ‘Run’. This is NOT done in the ‘Run Debug’. The script file is evaluated as it is. The user is responsible for the imports.
- In ‘Run Debug’ the script output is not send to the QuPath ScriptEditor but to the Eclipse Console and it is send to the Eclipse Console without additional format steps such as adding ‘\n’. The user should add ‘\n’ wherever it is helpful.
- Complex processes are slower in Debug mode.
