This is a follow up post, first part: Plugin not executed from Jython in headless mode
I am still having problems with the script syntax. The plugin returns an image that I want to save as a new file. I created a repository to demonstrate what I want to do:
I can save the image to the original location with this Jython code:
# @IOService io
# @CommandService command
# @ModuleService module
from my.test import TestPlugin
inpath = "/home/random/Development/imagej/plugins/fiji-plugin-script-example/script/blobs.tif"
myinput = io.open(inpath)
myfuture = command.run(TestPlugin, True, "input", myinput)
mymodule = module.waitFor(myfuture)
myoutput = mymodule.getOutput("output")
io.save(myoutput, inpath)
… but I cannot save it to a yet non existing file. Script code:
# @IOService io
# @CommandService command
# @ModuleService module
from my.test import TestPlugin
inpath = "/home/random/Development/imagej/plugins/fiji-plugin-script-example/script/blobs.tif"
outpath = "/home/random/Development/imagej/plugins/fiji-plugin-script-example/script/out.tif"
myinput = io.open(inpath)
myfuture = command.run(TestPlugin, True, "input", myinput)
mymodule = module.waitFor(myfuture)
myoutput = mymodule.getOutput("output")
io.save(myoutput, outpath)
Error message:
[ERROR] null
Traceback (most recent call last):
File "/home/random/Development/imagej/plugins/fiji-plugin-script-example/script/run-plugin.py", line 15, in <module>
io.save(myoutput, outpath)
at io.scif.io.VirtualHandle.read(VirtualHandle.java:83)
at io.scif.io.RandomAccessInputStream.read(RandomAccessInputStream.java:437)
at io.scif.formats.KontronFormat$Checker.isFormat(KontronFormat.java:124)
at io.scif.AbstractChecker.isFormat(AbstractChecker.java:93)
at io.scif.services.DefaultFormatService.getFormatList(DefaultFormatService.java:342)
at io.scif.services.DefaultFormatService.getFormat(DefaultFormatService.java:317)
at io.scif.services.DefaultDatasetIOService.canOpen(DefaultDatasetIOService.java:83)
at io.scif.io.DatasetIOPlugin.supportsSave(DatasetIOPlugin.java:70)
at org.scijava.io.IOPlugin.supportsSave(IOPlugin.java:76)
at org.scijava.io.IOService.getSaver(IOService.java:66)
at org.scijava.io.DefaultIOService.save(DefaultIOService.java:80)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
java.lang.UnsupportedOperationException: java.lang.UnsupportedOperationException: Attempting to read or write from a io.scif.io.VirtualHandle. There is no source to operate on.
at org.python.core.Py.JavaError(Py.java:546)
at org.python.core.Py.JavaError(Py.java:537)
at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:188)
at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:204)
at org.python.core.PyObject.__call__(PyObject.java:496)
at org.python.core.PyObject.__call__(PyObject.java:500)
at org.python.core.PyMethod.__call__(PyMethod.java:156)
at org.python.pycode._pyx0.f$0(/home/random/Development/imagej/plugins/fiji-plugin-script-example/script/run-plugin.py:15)
at org.python.pycode._pyx0.call_function(/home/random/Development/imagej/plugins/fiji-plugin-script-example/script/run-plugin.py)
at org.python.core.PyTableCode.call(PyTableCode.java:167)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1386)
at org.python.core.__builtin__.eval(__builtin__.java:497)
at org.python.core.__builtin__.eval(__builtin__.java:501)
at org.python.util.PythonInterpreter.eval(PythonInterpreter.java:259)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:40)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at org.scijava.script.ScriptModule.run(ScriptModule.java:160)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.UnsupportedOperationException: Attempting to read or write from a io.scif.io.VirtualHandle. There is no source to operate on.
at io.scif.io.VirtualHandle.read(VirtualHandle.java:83)
at io.scif.io.RandomAccessInputStream.read(RandomAccessInputStream.java:437)
at io.scif.formats.KontronFormat$Checker.isFormat(KontronFormat.java:124)
at io.scif.AbstractChecker.isFormat(AbstractChecker.java:93)
at io.scif.services.DefaultFormatService.getFormatList(DefaultFormatService.java:342)
at io.scif.services.DefaultFormatService.getFormat(DefaultFormatService.java:317)
at io.scif.services.DefaultDatasetIOService.canOpen(DefaultDatasetIOService.java:83)
at io.scif.io.DatasetIOPlugin.supportsSave(DatasetIOPlugin.java:70)
at org.scijava.io.IOPlugin.supportsSave(IOPlugin.java:76)
at org.scijava.io.IOService.getSaver(IOService.java:66)
at org.scijava.io.DefaultIOService.save(DefaultIOService.java:80)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:186)
... 24 more
I can fix that by first copying the input file to the output location…
from java.io import File
from java.nio.file import Files
infile = File(inpath)
outfile = File(outpath)
if not(outfile.exists()):
Files.copy(infile.toPath(), outfile.toPath())
… but that is pretty bad.
What is the correct way to do this?
Also if someone could help out how to write a groovy script doing the same… or an IJ1 version… That could be added to the repository and be a useful resource to others as well. Op usage is documented very well in the Wiki and the tutorials, but I could not find too much on the CommandService. Maybe I looked at the wrong places…
