Re: [ImageJ-devel] jython scripting, No compatible service: io.scif.SCIFIOService

Mon, 24 Feb 2014 02:35:35 -0800 

Hi again,
here's my second try: I made a pom.xml (attached) and retrieved dependency jar files with: 

mvn dependency:copy-dependencies


But I still get the same error as before:


CP=`find /home/hajaalin/Software/mvn-IJ2/target/dependency -name '*.jar' 
|sed ':a;N;$!ba;s/\n/:/g'`
jython -Dpython.path=$CP 
/home/hajaalin/Software/fiji-20140219/Fiji.app/macros/imglib0.py 
/home/hajaalin/Data/Misha/composite1.ome.tif

[WARNING] Class pool is empty: forgot to call Thread#setClassLoader?
Traceback (most recent call last):

  File 
"/home/hajaalin/Software/fiji-20140219/Fiji.app/macros/imglib0.py", line 
16, in <module>

    io = ImgOpener()

    at 
org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:218)

...

java.lang.IllegalArgumentException: java.lang.IllegalArgumentException: 
No compatible service: io.scif.SCIFIOService




Now it's maybe only a matter of getting the versions for pom-scijava and 
ij-app right. How can I find out which version to use?


Thanks,
Harri


On 21/02/14 13:25, Harri Jäälinoja wrote:

Hi,


I started to learn about ImgLib2 for the purpose of creating scripts I 
can run headlessly. I would like to use jython since I already used 
that with ImageJ1. First I downloaded a recent Fiji version. My idea 
was that this would be the easiest way to get the dependencies 
(scifio, imglib2 etc.) right.


mkdir fiji-20140219
cd fiji-20140219/

wget 
http://jenkins.imagej.net/job/Stable-Fiji/lastSuccessfulBuild/artifact/fiji-linux64.tar.gz

tar xf fiji-linux64.tar.gz



Then I just put all the jar files in the Fiji distribution in one long 
variable and gave that as the classpath for Jython
CP=`find /home/hajaalin/Software/fiji-20140219/Fiji.app/jars -name 
'*.jar' |sed ':a;N;$!ba;s/\n/:/g'`


Here's my test script:

----- imglib0.py ------
import sys

#from io.scif.config import SCIFIOConfig
from io.scif.config import *
from io.scif.img import ImgIOException,ImgOpener

from java.io import File

from net.imglib2.img import Img
from net.imglib2.img.display.imagej import ImageJFunctions
from net.imglib2.type import NativeType
from net.imglib2.type.numeric import RealType

filename = sys.argv[1]

io = ImgOpener()
config = SCIFIOConfig()
config.imgOpenerSetImgModes( SCIFIOConfig.ImgMode.CELL )
img = io.openImg(filename)

ImageJFunctions.show( img )
---------------------------


When I run it, I get an error I've seen on the list before:


hajaalin@biotek973:~/Software/fiji-20140219/Fiji.app$ jython 
-Dpython.path=$CP macros/imglib0.py 
/home/hajaalin/Data/Misha/composite1.ome.tif

[WARNING] Class pool is empty: forgot to call Thread#setClassLoader?
Traceback (most recent call last):
  File "macros/imglib0.py", line 16, in <module>
    io = ImgOpener()

    at 
org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:218)
    at 
org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:172)
    at 
org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:149)

    at org.scijava.Context.<init>(Context.java:179)
    at org.scijava.Context.<init>(Context.java:121)
    at org.scijava.Context.<init>(Context.java:109)

    at 
io.scif.img.AbstractImgIOComponent.<init>(AbstractImgIOComponent.java:59)

    at io.scif.img.ImgOpener.<init>(ImgOpener.java:94)

    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native 
Method)
    at 
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
    at 
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

    at java.lang.reflect.Constructor.newInstance(Constructor.java:526)

    at 
org.python.core.PyReflectedConstructor.constructProxy(PyReflectedConstructor.java:163)



java.lang.IllegalArgumentException: 
java.lang.IllegalArgumentException: No compatible service: 
io.scif.SCIFIOService



If I try to run the script via Fiji, I don't get even that far:


hajaalin@biotek973:~/Software/fiji-20140219/Fiji.app$ ./ImageJ-linux64 
macros/imglib0.py /home/hajaalin/Data/Misha/composite1.ome.tif

Traceback (most recent call last):
  File "macros/imglib0.py", line 4, in <module>
    from io.scif.config import *
ImportError: No module named io


So now my questions are:
1. Is there a better way to get all the dependency jars?

2. Is there something wrong with my general setup (jython + script + 
required jars)?



Thanks, best regards,
Harri




--
__________________________________________________
Harri Jäälinoja
Light Microscopy Unit
Institute of Biotechnology, University of Helsinki
http://www.biocenter.helsinki.fi/bi/lmu/
+358 9 191 59370 fax +358 9 191 59366


<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0";
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
    http://maven.apache.org/xsd/maven-4.0.0.xsd";>
  <modelVersion>4.0.0</modelVersion>
 
  <parent>
    <groupId>org.scijava</groupId>
    <artifactId>pom-scijava</artifactId>
    <version>1.134</version>
  </parent>

  <groupId>sc.fiji</groupId>
  <artifactId>my-uber-library</artifactId>
  <version>2.0.0-SNAPSHOT</version>

  <dependencies>
    <dependency>
      <groupId>net.imagej</groupId>
      <artifactId>ij-app</artifactId>
      <version>2.0.0-SNAPSHOT</version>
    </dependency>
  </dependencies>


  <repositories>
    <!-- NB: for project parent -->
    <repository>
      <id>imagej.releases</id>
      <url>http://maven.imagej.net/content/repositories/releases</url>
    </repository>
  </repositories>

</project>


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