Release_10953: where to put loci_tools.jar

I cloned the release_10953 branch source code from Github and am trying to build and run in Windows 7. I followed the instructions at github.com/CellProfiler/CellPro … ion-for-PC and manually fixed the references to PIL in the source code. When I launch CP, the splash screen appears and is followed by the main GUI, however, I am receiving a number of Java-related errors in the terminal (see below). My guess is that I need to put loci_tools.jar and ij.jar (any others?) somewhere so CP can find them. Where should I put these java libraries?

I suspect this has been addressed in an earlier thread (or earlier install instructions), but I have not been able to find it. Apologies if this is so.

Thanks much

Frederick

C:\Users\flo\My Documents\Github\CellProfiler>python cellprofiler.py
Using jdk_home = C:\Program Files\Java\jdk1.7.0_11
Load ilastik Core
Failed to get class loci/common/Location
Exception in thread “Thread-0” java.lang.NoClassDefFoundError: loci/common/Location
Caused by: java.lang.ClassNotFoundException: loci.common.Location
at java.net.URLClassLoader$1.run(Unknown Source)
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
Bioformats version does not support directory cacheing
Failed to get class org/apache/log4j/BasicConfigurator
Exception in thread “Thread-0” java.lang.NoClassDefFoundError: org/apache/log4j/BasicConfigurator
Caused by: java.lang.ClassNotFoundException: org.apache.log4j.BasicConfigurator
at java.net.URLClassLoader$1.run(Unknown Source)
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
Failed to initialize log4j
Traceback (most recent call last):
File “C:\Users\flo\My Documents\Github\CellProfiler\bioformats_init_.py”, line 132, in
“configure”, “()V”)
File “C:\Users\flo\My Documents\Github\CellProfiler\cellprofiler\utilities\jutil.py”, line 391, in static_call
raise JavaException(jexception)
JavaException: org/apache/log4j/BasicConfigurator
Failed to get class loci/formats/FormatTools
Failed to get class None
Traceback (most recent call last):
File “C:\Users\flo\My Documents\Github\CellProfiler\cellprofiler\modules\loadimages.py”, line 64, in
FormatTools = formatreader.make_format_tools_class()
File “C:\Users\flo\My Documents\Github\CellProfiler\bioformats\formatreader.py”, line 45, in make_format_tools_class
class FormatTools(object):
File “C:\Users\flo\My Documents\Github\CellProfiler\bioformats\formatreader.py”, line 52, in FormatTools
CAN_GROUP = jutil.get_static_field(klass, ‘CAN_GROUP’,‘I’)
File “C:\Users\flo\My Documents\Github\CellProfiler\cellprofiler\utilities\jutil.py”, line 458, in get_static_field
raise ValueError(“Could not load class %s”%class_name)
ValueError: Could not load class None

Hi Frederick,

10953 was a long time back! But assuming you really want to use that 2+ year old version…

loci_tools.jar goes here:
\bioformats
e.g. D:\Program Files\CellProfiler\bioformats

ij.jar goes here:
\imagej
e.g. D:\Program Files\CellProfiler\imagej

Also, make sure that you have set both your plugins directories (CellProfiler and ImageJ) properly in File>Preferences.

Good luck!
David