CellProfiler
How to install in readme
It would be great if there were installation instructions. For example, the right version of java has to be installed first, otherwise, just 'pip install python-bioformats' will fail.
I'm trying to get rid of all log4j output in the terminal when using python-bioformats. The following used to work, but apparently, after reinstall of the os, java, python and python-bioformats, it doesn't anymore since it can't find the jar for log4j even when log4j1.2 and log4j2 are installed (on Ubuntu 20.04).
import javabridge, bioformats javabridge.start_vm(class_path=bioformats.JARS, run_headless=True) log4j = javabridge.JClassWrapper("loci.common.Log4jTools") log4j.enableLogging() log4j.setRootLevel("ERROR")
The following is spit out to the terminal when calling log4j.enableLogging():
11:21:03.711 [Thread-0] DEBUG loci.common.ReflectedUniverse - No such class: org.apache.log4j.Level java.lang.ClassNotFoundException: org.apache.log4j.Level at java.net.URLClassLoader.findClass(URLClassLoader.java:382) ~[na:1.8.0_282] at java.lang.ClassLoader.loadClass(ClassLoader.java:418) ~[na:1.8.0_282] at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352) ~[na:1.8.0_282] at java.lang.ClassLoader.loadClass(ClassLoader.java:351) ~[na:1.8.0_282] at java.lang.Class.forName0(Native Method) ~[na:1.8.0_282] at java.lang.Class.forName(Class.java:348) ~[na:1.8.0_282] at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:174) ~[bioformats_package.jar:6.6.0] at loci.common.Log4jTools.enableLogging(Log4jTools.java:92) [bioformats_package.jar:6.6.0] 11:21:03.716 [Thread-0] DEBUG loci.common.ReflectedUniverse - No such class: org.apache.log4j.Level java.lang.ClassNotFoundException: org.apache.log4j.Level at java.net.URLClassLoader.findClass(URLClassLoader.java:382) ~[na:1.8.0_282] at java.lang.ClassLoader.loadClass(ClassLoader.java:418) ~[na:1.8.0_282] at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352) ~[na:1.8.0_282] at java.lang.ClassLoader.loadClass(ClassLoader.java:351) ~[na:1.8.0_282] at java.lang.Class.forName0(Native Method) ~[na:1.8.0_282] at java.lang.Class.forName(Class.java:348) ~[na:1.8.0_282] at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:174) ~[bioformats_package.jar:6.6.0] at loci.common.Log4jTools.setRootLevel(Log4jTools.java:73) [bioformats_package.jar:6.6.0]
