Re: [scipion-users] Error in xmipp particle picking

[Jose M. de la R. T. <del...@gm...>]

Dear Ashutosh,

Thanks for re-sending your mail to this list. We will try to reproduce your
problem and let you know.

Bests,
Jose Miguel.


On Thu, Sep 15, 2016 at 2:00 PM, ashutosh srivastava <ash...@gm...>
wrote:

> Dear Scipion and xmipp users
>
> I posted the following in newxmipp users list which I have now learnt is
> no longer active, so this is a repost. Sorry if this gets repeated in your
> inbox.
>
>
> I am trying to pick particles from imported micrographs in Scipion GUI,
> but keep getting this error
> "No enum constant xmipp.viewer.particlepicker.training.model.Mode"
> Following are some relevant details.
> Micrographs imported from tif files and import finished without any
> errors, I can see the micrographs with in scipion.
> The xmipp3-manual-picking (step1) application dialogue box opens and I can
> enter the micrograph location, however upon execution the above mentioned
> error pops up. Following gets echoed on terminal
>
> *java.lang.IllegalArgumentException: No enum constant
> xmipp.viewer.particlepicker.tr
> <http://xmipp.viewer.particlepicker.tr>aining.model.Mode.*
> * at xmipp.viewer.particlepicker.tr
> <http://xmipp.viewer.particlepicker.tr>aining.model.SupervisedParticlePicker.loadConfig(SupervisedParticlePicker.java:638)*
> * at xmipp.viewer.particlepicker.Pa
> <http://xmipp.viewer.particlepicker.Pa>rticlePicker.<init>(ParticlePicker.java:149)*
> * at xmipp.viewer.particlepicker.tr
> <http://xmipp.viewer.particlepicker.tr>aining.model.SupervisedParticlePicker.<init>(SupervisedParticlePicker.java:79)*
> * at xmipp.viewer.particlepicker.tr
> <http://xmipp.viewer.particlepicker.tr>aining.model.SupervisedParticlePicker.<init>(SupervisedParticlePicker.java:72)*
> * at xmipp.viewer.particlepicker.tr
> <http://xmipp.viewer.particlepicker.tr>aining.model.SupervisedParticlePicker.<init>(SupervisedParticlePicker.java:125)*
> * at xmipp.viewer.particlepicker.tr
> <http://xmipp.viewer.particlepicker.tr>aining.SupervisedPickerRunner.run(SupervisedPickerRunner.java:33)*
> * at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)*
> * at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)*
> * at java.awt.EventQueue.access$500(EventQueue.java:97)*
> * at java.awt.EventQueue$3.run(EventQueue.java:709)*
> * at java.awt.EventQueue$3.run(EventQueue.java:703)*
> * at java.security.AccessController.doPrivileged(Native Method)*
> * at
> java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)*
> * at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)*
> * at
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)*
> * at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)*
> * at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)*
> * at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)*
> * at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)*
> * at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)*
>
> In the terminal following warnings keep repeating
>
> *WARNING: MetaData: Error parsing column 'particleSize' value.*
> *WARNING: MetaData: Error parsing column 'autopickPercent' value.*
> *WARNING: MetaData: Error parsing column 'templatesNum' value.*
> *WARNING: MetaData: Error parsing column 'pickingState' value.*
> *WARNING: MetaData: Error parsing column 'manualParticlesNum' value.*
> *WARNING: MetaData: Error parsing column 'autoParticlesNum' value.*
> *WARNING!!! valueIn.failed = True, binding NULL*
> *WARNING!!! valueIn.failed = True, binding NULL*
> *WARNING!!! valueIn.failed = True, binding NULL*
> *WARNING!!! valueIn.failed = True, binding NULL*
> *WARNING!!! valueIn.failed = True, binding NULL*
> *WARNING!!! valueIn.failed = True, binding NULL*
>
> I am using scipion v1.0.0 and in the current project I just imported the
> micrographs and then particle picking.
> I can still open the interactive manual picking run in earlier projects as
> well as I can start a new manual picking run in older already saved
> projects (in which the picking has already been done). It seems the problem
> occurs when I am trying to start a new particle picking run in a new
> project.
> The general config file looks like following, where /path/to/mpi is my
> path to mpi. However, since earlier projects are running fine I think its
> unlikely that the problem lies here.
>
> SCIPION_URL = http://scipion.cnb.csic.es/downloads/scipion
> SCIPION_URL_TESTDATA = %(SCIPION_URL)s/data/tests
> SCIPION_URL_SOFTWARE = %(SCIPION_URL)s/software
>
> [DIRS_GLOBAL]
> SCIPION_SOFTWARE = software
> SCIPION_TESTS = data/tests
>
> [BUILD]
> LINKERFORPROGRAMS = g++
> CXXFLAGS =
> GTEST = False
> MPI_LINKERFORPROGRAMS = mpiCC
> MPI_LIB = openmpi
> MPI_BINDIR = path/to/mpi/bin
> JNI_CPPPATH = %(JAVA_HOME)s/include:%(JAVA_HOME)s/include/linux
> OPENCV = True
> MPI_CC = mpicc
> CUDA = False
> JAVA_HOME = /usr/lib/jvm/java-1.8.0-openjdk
> MATLAB = False
> JAVA_BINDIR = %(JAVA_HOME)s/bin
> CC = gcc
> JAR = %(JAVA_BINDIR)s/jar
> MPI_CXX = mpiCC
> DEBUG = False
> MPI_LIBDIR = /path/to/mpi/lib
> JAVAC = %(JAVA_BINDIR)s/javac
> CXX = g++
> LINKFLAGS =
> CCFLAGS = -std=c99
> MATLAB_DIR = /usr/local/MATLAB/R2011a
> MPI_INCLUDE = /path/to/mpi/include
>
> Thank you. Kindly let me know if any more details are required.
>
> Best Regards
> Ashutosh
>
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