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error in bfopen in MATLAB 2014b on mac

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error in bfopen in MATLAB 2014b on mac

Postby een1dae » Wed Nov 12, 2014 11:28 am

Error message from bfopen using MATLAB 2014b on Mac.

When attempting to import a flex file into MATLAB using bfopen, I receive the error message:

Undefined variable "loci" or class
"loci.common.DebugTools.enableLogging".

Error in bfopen (line 111)
loci.common.DebugTools.enableLogging('INFO');

The latest version of loci_tools in in the active directory. Can anyone explain what I have done incorrectly?

Many thanks
een1dae
 
Posts: 4
Joined: Fri Sep 13, 2013 9:50 am
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Re: error in bfopen in MATLAB 2014b on mac

Postby sbesson » Wed Nov 12, 2014 2:01 pm

Hi I cannot reproduce locally with Bio-Formats 5.0.5 and MATLAB R2014b,

what is the version of Bio-Formats you are using? What is the content of the Java class path?

Code: Select all
>> [~,v] = bfCheckJavaPath
>> javaclasspath


Best,
Sebastien
User avatar
sbesson
Team Member
 
Posts: 421
Joined: Tue Feb 28, 2012 7:20 pm
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Re: error in bfopen in MATLAB 2014b on mac

Postby een1dae » Thu Nov 13, 2014 10:56 am

Thanks for looking into this

v =

5.0.6

Applications/MATLAB_R2014b.app/java/patch
/Applications/MATLAB_R2014b.app/java/jarext/AnimatedTransitions.jar
/Applications/MATLAB_R2014b.app/java/jarext/ant.jar
/Applications/MATLAB_R2014b.app/java/jarext/ant-launcher.jar
/Applications/MATLAB_R2014b.app/java/jarext/antlr.jar
/Applications/MATLAB_R2014b.app/java/jarext/felix.jar
/Applications/MATLAB_R2014b.app/java/jarext/scr.jar
/Applications/MATLAB_R2014b.app/java/jarext/axis2/activation.jar
/Applications/MATLAB_R2014b.app/java/jarext/axis2/axiom-api.jar
/Applications/MATLAB_R2014b.app/java/jarext/axis2/axiom-impl.jar
/Applications/MATLAB_R2014b.app/java/jarext/axis2/axis2-adb.jar
/Applications/MATLAB_R2014b.app/java/jarext/axis2/axis2-kernel.jar
/Applications/MATLAB_R2014b.app/java/jarext/axis2/axis2-transport-http.jar
/Applications/MATLAB_R2014b.app/java/jarext/axis2/axis2-transport-local.jar
/Applications/MATLAB_R2014b.app/java/jarext/axis2/commons-httpclient.jar
/Applications/MATLAB_R2014b.app/java/jarext/axis2/geronimo-stax-api.jar
/Applications/MATLAB_R2014b.app/java/jarext/axis2/httpcore.jar
/Applications/MATLAB_R2014b.app/java/jarext/axis2/mail.jar
/Applications/MATLAB_R2014b.app/java/jarext/axis2/neethi.jar
/Applications/MATLAB_R2014b.app/java/jarext/axis2/wsdl4j.jar
/Applications/MATLAB_R2014b.app/java/jarext/axis2/wstx-asl.jar
/Applications/MATLAB_R2014b.app/java/jarext/axis2/XmlSchema.jar
/Applications/MATLAB_R2014b.app/java/jarext/batik-anim.jar
/Applications/MATLAB_R2014b.app/java/jarext/batik-extension.jar
/Applications/MATLAB_R2014b.app/java/jarext/batik-dom.jar
/Applications/MATLAB_R2014b.app/java/jarext/batik-transcoder.jar
/Applications/MATLAB_R2014b.app/java/jarext/batik-awt-util.jar
/Applications/MATLAB_R2014b.app/java/jarext/batik-bridge.jar
/Applications/MATLAB_R2014b.app/java/jarext/batik-gvt.jar
/Applications/MATLAB_R2014b.app/java/jarext/batik-css.jar
/Applications/MATLAB_R2014b.app/java/jarext/batik-parser.jar
/Applications/MATLAB_R2014b.app/java/jarext/batik-ext.jar
/Applications/MATLAB_R2014b.app/java/jarext/batik-gui-util.jar
/Applications/MATLAB_R2014b.app/java/jarext/batik-svggen.jar
/Applications/MATLAB_R2014b.app/java/jarext/batik-codec.jar
/Applications/MATLAB_R2014b.app/java/jarext/batik-svg-dom.jar
/Applications/MATLAB_R2014b.app/java/jarext/batik-script.jar
/Applications/MATLAB_R2014b.app/java/jarext/batik-util.jar
/Applications/MATLAB_R2014b.app/java/jarext/batik-swing.jar
/Applications/MATLAB_R2014b.app/java/jarext/batik-xml.jar
/Applications/MATLAB_R2014b.app/java/jarext/bluecove-bluez.jar
/Applications/MATLAB_R2014b.app/java/jarext/bluecove-emu.jar
/Applications/MATLAB_R2014b.app/java/jarext/bluecove.jar
/Applications/MATLAB_R2014b.app/java/jarext/chilkat/chilkat.jar
/Applications/MATLAB_R2014b.app/java/jarext/commons-cli.jar
/Applications/MATLAB_R2014b.app/java/jarext/commons-codec.jar
/Applications/MATLAB_R2014b.app/java/jarext/commons-collections-generic.jar
/Applications/MATLAB_R2014b.app/java/jarext/commons-collections.jar
/Applications/MATLAB_R2014b.app/java/jarext/commons-compress.jar
/Applications/MATLAB_R2014b.app/java/jarext/commons-io.jar
/Applications/MATLAB_R2014b.app/java/jarext/commons-lang.jar
/Applications/MATLAB_R2014b.app/java/jarext/commons-logging.jar
/Applications/MATLAB_R2014b.app/java/jarext/commons-math.jar
/Applications/MATLAB_R2014b.app/java/jarext/commons-net.jar
/Applications/MATLAB_R2014b.app/java/jarext/dom4j.jar
/Applications/MATLAB_R2014b.app/java/jarext/emma_ant.jar
/Applications/MATLAB_R2014b.app/java/jarext/emma.jar
/Applications/MATLAB_R2014b.app/java/jarext/fop.jar
/Applications/MATLAB_R2014b.app/java/jarext/avalon-framework.jar
/Applications/MATLAB_R2014b.app/java/jarext/foxtrot.jar
/Applications/MATLAB_R2014b.app/java/jarext/geotools/geoapi-nogenerics.jar
/Applications/MATLAB_R2014b.app/java/jarext/geotools/gt2-api.jar
/Applications/MATLAB_R2014b.app/java/jarext/geotools/gt2-coverage.jar
/Applications/MATLAB_R2014b.app/java/jarext/geotools/gt2-main.jar
/Applications/MATLAB_R2014b.app/java/jarext/geotools/gt2-referencing.jar
/Applications/MATLAB_R2014b.app/java/jarext/geotools/gt2-referencing3D.jar
/Applications/MATLAB_R2014b.app/java/jarext/geotools/gt2-wms.jar
/Applications/MATLAB_R2014b.app/java/jarext/geotools/jts.jar
/Applications/MATLAB_R2014b.app/java/jarext/glazedlists_java15.jar
/Applications/MATLAB_R2014b.app/java/jarext/google-collect.jar
/Applications/MATLAB_R2014b.app/java/jarext/guice/aopalliance.jar
/Applications/MATLAB_R2014b.app/java/jarext/guice/guice.jar
/Applications/MATLAB_R2014b.app/java/jarext/guice/guice-assistedinject.jar
/Applications/MATLAB_R2014b.app/java/jarext/guice/javax.inject.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/h2.jar
/Applications/MATLAB_R2014b.app/java/jarext/ice/ice.jar
/Applications/MATLAB_R2014b.app/java/jarext/ice/ib6core.jar
/Applications/MATLAB_R2014b.app/java/jarext/ice/ib6extra.jar
/Applications/MATLAB_R2014b.app/java/jarext/ice/ib6http.jar
/Applications/MATLAB_R2014b.app/java/jarext/ice/ib6https.jar
/Applications/MATLAB_R2014b.app/java/jarext/ice/ib6js.jar
/Applications/MATLAB_R2014b.app/java/jarext/ice/ib6swing.jar
/Applications/MATLAB_R2014b.app/java/jarext/ice/ib6util.jar
/Applications/MATLAB_R2014b.app/java/jarext/ice/ib6xalan.jar
/Applications/MATLAB_R2014b.app/java/jarext/ice/icessl.jar
/Applications/MATLAB_R2014b.app/java/jarext/access-bridge.jar
/Applications/MATLAB_R2014b.app/java/jarext/jaccess-1_4.jar
/Applications/MATLAB_R2014b.app/java/jarext/jaxen.jar
/Applications/MATLAB_R2014b.app/java/jarext/jdom.jar
/Applications/MATLAB_R2014b.app/java/jarext/annotations.jar
/Applications/MATLAB_R2014b.app/java/jarext/jgit/jgit.jar
/Applications/MATLAB_R2014b.app/java/jarext/jgit/jgitui.jar
/Applications/MATLAB_R2014b.app/java/jarext/jgoodies-forms.jar
/Applications/MATLAB_R2014b.app/java/jarext/jgoodies-looks.jar
/Applications/MATLAB_R2014b.app/java/jarext/jide/jide-action.jar
/Applications/MATLAB_R2014b.app/java/jarext/jide/jide-charts.jar
/Applications/MATLAB_R2014b.app/java/jarext/jide/jide-common.jar
/Applications/MATLAB_R2014b.app/java/jarext/jide/jide-components.jar
/Applications/MATLAB_R2014b.app/java/jarext/jide/jide-dialogs.jar
/Applications/MATLAB_R2014b.app/java/jarext/jide/jide-dock.jar
/Applications/MATLAB_R2014b.app/java/jarext/jide/jide-properties.jar
/Applications/MATLAB_R2014b.app/java/jarext/jide/jide-grids.jar
/Applications/MATLAB_R2014b.app/java/jarext/jide/jide-shortcut.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/fiddler-dl.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/phoenix-dl.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/mahalo.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/destroy.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/jsk-platform.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/jini-ext.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/jini-core.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/reggie-dl.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/norm-dl.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/browser-dl.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/sdm-dl.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/norm.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/mahalo-dl.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/group.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/phoenix-init.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/browser.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/reggie.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/fiddler.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/phoenix-group.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/sun-util.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/jsk-policy.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/group-dl.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/sharedvm.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/start.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/jsk-resources.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/jini2/lib/phoenix.jar
/Applications/MATLAB_R2014b.app/java/jarext/Jmol.jar
/Applications/MATLAB_R2014b.app/java/jarext/Acme.jar
/Applications/MATLAB_R2014b.app/java/jarext/gluegen-rt.jar
/Applications/MATLAB_R2014b.app/java/jarext/jogl-all.jar
/Applications/MATLAB_R2014b.app/java/jarext/jsch.jar
/Applications/MATLAB_R2014b.app/java/jarext/jung/jung-3d.jar
/Applications/MATLAB_R2014b.app/java/jarext/jung/jung-algorithms.jar
/Applications/MATLAB_R2014b.app/java/jarext/jung/jung-api.jar
/Applications/MATLAB_R2014b.app/java/jarext/jung/jung-graph-impl.jar
/Applications/MATLAB_R2014b.app/java/jarext/jung/jung-io.jar
/Applications/MATLAB_R2014b.app/java/jarext/jung/jung-jai.jar
/Applications/MATLAB_R2014b.app/java/jarext/jung/jung-visualization.jar
/Applications/MATLAB_R2014b.app/java/jarext/jxbrowser-chromium/jxbrowser-chromium.jar
/Applications/MATLAB_R2014b.app/java/jarext/jxbrowser-chromium/runtime.jar
/Applications/MATLAB_R2014b.app/java/jarext/jxbrowser/comfyj.jar
/Applications/MATLAB_R2014b.app/java/jarext/jxbrowser/engine-gecko.jar
/Applications/MATLAB_R2014b.app/java/jarext/jxbrowser/engine-gecko15.jar
/Applications/MATLAB_R2014b.app/java/jarext/jxbrowser/engine-ie.jar
/Applications/MATLAB_R2014b.app/java/jarext/jxbrowser/engine-webkit.jar
/Applications/MATLAB_R2014b.app/java/jarext/jxbrowser/jniwrap.jar
/Applications/MATLAB_R2014b.app/java/jarext/jxbrowser/jxbrowser.jar
/Applications/MATLAB_R2014b.app/java/jarext/jxbrowser/runtime.jar
/Applications/MATLAB_R2014b.app/java/jarext/jxbrowser/winpack.jar
/Applications/MATLAB_R2014b.app/java/jarext/jxlayer.jar
/Applications/MATLAB_R2014b.app/java/jarext/log4j.jar
/Applications/MATLAB_R2014b.app/java/jarext/lucene-analyzers-common.jar
/Applications/MATLAB_R2014b.app/java/jarext/lucene-core.jar
/Applications/MATLAB_R2014b.app/java/jarext/lucene-queryparser.jar
/Applications/MATLAB_R2014b.app/java/jarext/nekohtml.jar
/Applications/MATLAB_R2014b.app/java/jarext/openxml4j.jar
/Applications/MATLAB_R2014b.app/java/jarext/rfa.jar
/Applications/MATLAB_R2014b.app/toolbox/datafeed/datafeed/config_editor.jar
/Applications/MATLAB_R2014b.app/java/jarext/RXTXcomm.jar
/Applications/MATLAB_R2014b.app/java/jarext/saxon9-ant.jar
/Applications/MATLAB_R2014b.app/java/jarext/saxon9-dom.jar
/Applications/MATLAB_R2014b.app/java/jarext/saxon9-dom4j.jar
/Applications/MATLAB_R2014b.app/java/jarext/saxon9-jdom.jar
/Applications/MATLAB_R2014b.app/java/jarext/saxon9-s9api.jar
/Applications/MATLAB_R2014b.app/java/jarext/saxon9-sql.jar
/Applications/MATLAB_R2014b.app/java/jarext/saxon9-xom.jar
/Applications/MATLAB_R2014b.app/java/jarext/saxon9-xpath.jar
/Applications/MATLAB_R2014b.app/java/jarext/saxon9-xqj.jar
/Applications/MATLAB_R2014b.app/java/jarext/saxon9.jar
/Applications/MATLAB_R2014b.app/java/jarext/slf4j/slf4j-api.jar
/Applications/MATLAB_R2014b.app/java/jarext/slf4j/slf4j-log4j12.jar
/Applications/MATLAB_R2014b.app/java/jarext/sqlite4java/sqlite4java.jar
/Applications/MATLAB_R2014b.app/java/jarext/svnkit/svnkit.jar
/Applications/MATLAB_R2014b.app/java/jarext/svnkit/svnkit-cli.jar
/Applications/MATLAB_R2014b.app/java/jarext/svnkit/sqljet.jar
/Applications/MATLAB_R2014b.app/java/jarext/svnkit/jna.jar
/Applications/MATLAB_R2014b.app/java/jarext/svnkit/trilead.jar
/Applications/MATLAB_R2014b.app/java/jarext/svnkit/sequence.jar
/Applications/MATLAB_R2014b.app/java/jarext/tablelayout.jar
/Applications/MATLAB_R2014b.app/java/jarext/TimingFramework.jar
/Applications/MATLAB_R2014b.app/java/jarext/j2ee/jsp-api.jar
/Applications/MATLAB_R2014b.app/java/jarext/j2ee/servlet-api.jar
/Applications/MATLAB_R2014b.app/java/jarext/webrenderer.jar
/Applications/MATLAB_R2014b.app/java/jarext/distcomp/wrapper.jar
/Applications/MATLAB_R2014b.app/java/jarext/xercesImpl.jar
/Applications/MATLAB_R2014b.app/java/jarext/xml-apis.jar
/Applications/MATLAB_R2014b.app/java/jarext/xml-apis-ext.jar
/Applications/MATLAB_R2014b.app/java/jarext/xmlgraphics-commons.jar
/Applications/MATLAB_R2014b.app/java/jarext/xstream.jar
/Applications/MATLAB_R2014b.app/java/jar/instwiz.jar
/Applications/MATLAB_R2014b.app/java/jar/addons_app.jar
/Applications/MATLAB_R2014b.app/java/jar/addons_product.jar
/Applications/MATLAB_R2014b.app/java/jar/addons_search_path_writer.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/parallel/admincenter.jar
/Applications/MATLAB_R2014b.app/java/jar/appmanagement.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/apps.jar
/Applications/MATLAB_R2014b.app/java/jar/bde.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/bioinfo.jar
/Applications/MATLAB_R2014b.app/java/jarext/webservices/cloud_console/cloud-console-client.jar
/Applications/MATLAB_R2014b.app/java/jar/cmlink/api.jar
/Applications/MATLAB_R2014b.app/java/jar/cmlink/util.jar
/Applications/MATLAB_R2014b.app/java/jar/cmlink/implementations/localcm.jar
/Applications/MATLAB_R2014b.app/java/jar/cmlink/implementations/svncore.jar
/Applications/MATLAB_R2014b.app/java/jar/cmlink/implementations/svnintegration.jar
/Applications/MATLAB_R2014b.app/java/jar/cmlink/implementations/svnkitintegration.jar
/Applications/MATLAB_R2014b.app/java/jar/cmlink/implementations/git.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/coder.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/comm.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/shared/computils.jar
/Applications/MATLAB_R2014b.app/java/jar/comparisons.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/compiler.jar
/Applications/MATLAB_R2014b.app/java/jarext/connector_api/connector_api_java/connector_interface.jar
/Applications/MATLAB_R2014b.app/java/jarext/connector_api/connector_api_java/message_service_interface.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/curvefit.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/database.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/datafeed.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/distcomp.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/dsp.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/eml.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/fixedpoint.jar
/Applications/MATLAB_R2014b.app/java/jar/foundation_libraries.jar
/Applications/MATLAB_R2014b.app/java/jarext/webservices/gds_client/mw-gds-client.jar
/Applications/MATLAB_R2014b.app/java/jarext/webservices/gds_jobs_client/gds-jobs-client.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/geoweb.jar
/Applications/MATLAB_R2014b.app/java/jar/hwsmanagement.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/idelink/extensions/eclipseide.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/idelink/extensions/armtoolchain.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/ident.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/images.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/imaq.jar
/Applications/MATLAB_R2014b.app/java/jar/install.jar
/Applications/MATLAB_R2014b.app/java/jar/installwizard.jar
/Applications/MATLAB_R2014b.app/java/jar/wizard.jar
/Applications/MATLAB_R2014b.app/java/jar/installbundle.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/instrument.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/activation_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/admincenter_jar_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/appmanagement_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/apps_java_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/cmlink_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/coder_java_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/comp_utils_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/comparisons_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/compiler_java_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/curvefit_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/distcomp_jar_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/dsp_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/eml_java_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/fixedpoint_java_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/hwsmanagement_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/images_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/install_api_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/install_core_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/instrument_java_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/javabuilder_java_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/lmlogin_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/matlab_addons_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/matlab_desktop_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/matlab_graphics_java_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/matlab_graphics_java_widgets_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/matlab_java_core_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/matlab_java_project_impl_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/matlab_java_widgets_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/matlab_sourcecontrol_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/mw_java_foundation_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/mw_java_help_ui_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/mw_java_html_res.jar
/Applications/MATLAB_R2014b.app/java/jar/ja_JP/optim_res.jar
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/Applications/MATLAB_R2014b.app/java/jar/toolbox/simulink/iomanager.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/simulink/linkstool.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/simulink/lookuptable.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/simulink/maskeditor.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/simulink/mdlrefsignallog.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/simulink/preferences.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/simulink/progressbar.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/simulink/sfunbuilder.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/simulink/signalselector.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/simulink/signalviewer.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/simulink/sigselector.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/simulink/variantmanager.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/mdldisc.jar
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/Applications/MATLAB_R2014b.app/java/jar/toolbox/simulink/sta.jar
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/Applications/MATLAB_R2014b.app/java/jar/toolbox/slestim.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/sldo.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/slproject.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/stateflow.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/stats.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/stm.jar
/Applications/MATLAB_R2014b.app/java/jar/storage/gdsinmatlab.jar
/Applications/MATLAB_R2014b.app/java/jar/storage/gds.jar
/Applications/MATLAB_R2014b.app/java/jar/storage/provider.jar
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/Applications/MATLAB_R2014b.app/java/jar/storage/filesystemadapter.jar
/Applications/MATLAB_R2014b.app/java/jar/supportsoftwareinstaller.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/symbolic.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/timeseries.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox_packaging.jar
/Applications/MATLAB_R2014b.app/java/jar/toolboxmanagement.jar
/Applications/MATLAB_R2014b.app/java/jar/trialsinstaller.jar
/Applications/MATLAB_R2014b.app/java/jarext/webservices/udc_client/udc_client.jar
/Applications/MATLAB_R2014b.app/java/jarext/webservices/udc_client_installer/udc_client_installer.jar
/Applications/MATLAB_R2014b.app/java/jar/toolbox/vision.jar
/Applications/MATLAB_R2014b.app/java/jar/mlwebservices.jar
/Applications/MATLAB_R2014b.app/java/jar/net.jar
/Applications/MATLAB_R2014b.app/java/jar/webproxy.jar
/Applications/MATLAB_R2014b.app/java/jar/webintegration.jar
/Applications/MATLAB_R2014b.app/java/jarext/webservices/ws_client_core/mw-service-client-core.jar
/Applications/MATLAB_R2014b.app/java/jarext/mwaws_client.jar
/Applications/MATLAB_R2014b.app/java/jarext/dws_client.jar
/Applications/MATLAB_R2014b.app/java/jarext/webservices/loginws_client.jar
/Applications/MATLAB_R2014b.app/java/jarext/webservices/service_request_client.jar
/Applications/MATLAB_R2014b.app/java/jarext/webservices/dws_client.jar
/Applications/MATLAB_R2014b.app/java/jarext/webservices/ws_usagedata_client/usagedata-client.jar
/Applications/MATLAB_R2014b.app/java/jar/zh_CN/activation_res.jar
/Applications/MATLAB_R2014b.app/java/jar/zh_CN/install_api_res.jar
/Applications/MATLAB_R2014b.app/java/jar/zh_CN/install_core_res.jar
/Applications/MATLAB_R2014b.app/java/jar/zh_CN/professional_activation_res.jar
/Applications/MATLAB_R2014b.app/java/jar/zh_CN/shared_install_res.jar
/Applications/MATLAB_R2014b.app/java/jar/zh_CN/web_connectivity_res.jar

DYNAMIC JAVA PATH

/Users/eendae/Documents/MATLAB/bfmatlab/bioformats_package.jar
een1dae
 
Posts: 4
Joined: Fri Sep 13, 2013 9:50 am
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Re: error in bfopen in MATLAB 2014b on mac

Postby sbesson » Thu Nov 13, 2014 3:51 pm

Hi,

this is really surprising because the version returned means the library is correctly loaded. Does

Code: Select all
r=bfGetReader('/path/to/the/flex.flex');



also fail with an Undefined variable or class exception?

Sebastien
User avatar
sbesson
Team Member
 
Posts: 421
Joined: Tue Feb 28, 2012 7:20 pm
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Re: error in bfopen in MATLAB 2014b on mac

Postby een1dae » Fri Nov 14, 2014 3:36 pm

That seems to work without any problems

>> filename = '~/Desktop/20141030_32_VCC_analogs_Ube2C/001020000.flex';
>> r=bfGetReader(filename);
>> r

r =

loci.formats.ChannelSeparator@6a7574b4
een1dae
 
Posts: 4
Joined: Fri Sep 13, 2013 9:50 am
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Re: error in bfopen in MATLAB 2014b on mac

Postby sbesson » Fri Nov 14, 2014 4:00 pm

So the problem seems to lie with the loading of this particular class or package. Does another class of the package, for instance,

Code: Select all
loci.common.DataTools.bytesToShort(1,false);


fail with a similar error?

If not, can you run the Java imports without problem from the MATLAB command prompt?

Code: Select all
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.PrintStream;
import java.lang.reflect.Field;
import java.lang.reflect.Method;
import java.lang.reflect.Modifier;
import java.util.Arrays;


Sebastien
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sbesson
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