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jefferis / fiji-cmtk-gui

Simple GUI frontend for CMTK image registration tools in Fiji/ImageJ
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Problems with installing on Windows #18

Open CarolaSt opened 6 years ago

CarolaSt commented 6 years ago

Hi Gregory,

I am having problems installing the Fiji CMTK gui on a Windows computer (I tried Windows 7 and Windows 10). I followed the direction as outlined in the readme file but when I try to run 'Install CMTK' a Java console window opens and I get the following error message (see below). I am rather a novice with image registration and it could be that there is an easy fix. Any suggestions for trouble shooting would be really helpful. Thank you very much for your help.

Best, Carola

console: Failed to install '': java.nio.charset.UnsupportedCharsetException: cp0. [ERROR] null Traceback (most recent call last): File "CMTK_Registration/Install_CMTK.py", line 11, in File "C:\FIJI-W~1\Fiji.app\plugins\CMTK_Registration\cmtkgui.py", line 5, in import subprocess, re, urllib2, tempfile File "C:\FIJI-W~1\Fiji.app\jars\jython-shaded-2.7.1.jar\Lib\subprocess.py", line 799, in File "C:\FIJI-W~1\Fiji.app\jars\jython-shaded-2.7.1.jar\Lib\subprocess.py", line 1399, in Popen File "C:\FIJI-W~1\Fiji.app\jars\jython-shaded-2.7.1.jar\Lib\ctypes__init.py", line 281, in getattr File "C:\FIJI-W~1\Fiji.app\jars\jython-shaded-2.7.1.jar\Lib\ctypes\init.py", line 262, in init__ at org.scijava.jython.shaded.com.kenai.jffi.Foreign.newLoadError(Foreign.java:72) at org.scijava.jython.shaded.com.kenai.jffi.Foreign.access$300(Foreign.java:42) at org.scijava.jython.shaded.com.kenai.jffi.Foreign$InValidInstanceHolder.getForeign(Foreign.java:98) at org.scijava.jython.shaded.com.kenai.jffi.Foreign.getInstance(Foreign.java:103) at org.scijava.jython.shaded.com.kenai.jffi.Library.openLibrary(Library.java:157) at org.scijava.jython.shaded.com.kenai.jffi.Library.getCachedInstance(Library.java:131) at org.python.modules.jffi.DynamicLibrary.(DynamicLibrary.java:26) at org.python.modules.jffi.jffi.dlopen(jffi.java:43) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:497) java.lang.UnsatisfiedLinkError: java.lang.UnsatisfiedLinkError: org.scijava.jython.shaded.com.kenai.jffi.Foreign.getVersion()I

at org.python.core.Py.JavaError(Py.java:552) at org.python.core.Py.JavaError(Py.java:543) at org.python.core.PyReflectedFunction.call(PyReflectedFunction.java:190) at org.python.core.PyReflectedFunction.call(PyReflectedFunction.java:206) at org.python.core.PyObject.call(PyObject.java:497) at org.python.core.PyObject.call(PyObject.java:501) at ctypes$py.init$49(C:/FIJI-W~1/Fiji.app/jars/jython-shaded-2.7.1.jar/Lib/ctypes/init.py:262) at ctypes$py.call_function(C:/FIJI-W~1/Fiji.app/jars/jython-shaded-2.7.1.jar/Lib/ctypes/init.py) at org.python.core.PyTableCode.call(PyTableCode.java:171) at org.python.core.PyBaseCode.call(PyBaseCode.java:308) at org.python.core.PyBaseCode.call(PyBaseCode.java:199) at org.python.core.PyFunction.call(PyFunction.java:482) at org.python.core.PyFunction.call(PyFunction.java:476) at org.python.core.PyInstance.init(PyInstance.java:124) at org.python.core.PyClass.call(PyClass.java:193) at org.python.core.PyObject.call(PyObject.java:480) at org.python.core.PyObject.call(PyObject.java:484) at ctypes$py.getattr$54(C:/FIJI-W~1/Fiji.app/jars/jython-shaded-2.7.1.jar/Lib/ctypes/init.py:283) at ctypes$py.call_function(C:/FIJI-W~1/Fiji.app/jars/jython-shaded-2.7.1.jar/Lib/ctypes/init.py) at org.python.core.PyTableCode.call(PyTableCode.java:171) at org.python.core.PyBaseCode.call(PyBaseCode.java:154) at org.python.core.PyFunction.call(PyFunction.java:423) at org.python.core.PyMethod.call(PyMethod.java:141) at org.python.core.PyMethod.call(PyMethod.java:132) at org.python.core.Deriveds.findattr_ex(Deriveds.java:81) at org.python.core.PyObjectDerived.findattr_ex(PyObjectDerived.java:1036) at org.python.core.PyObject.getattr(PyObject.java:1025) at subprocess$py.Popen$22(C:/FIJI-W~1/Fiji.app/jars/jython-shaded-2.7.1.jar/Lib/subprocess.py:1886) at subprocess$py.call_function(C:/FIJI-W~1/Fiji.app/jars/jython-shaded-2.7.1.jar/Lib/subprocess.py) at org.python.core.PyTableCode.call(PyTableCode.java:171) at org.python.core.PyBaseCode.call(PyBaseCode.java:308) at org.python.core.Py.makeClass(Py.java:2066) at org.python.core.Py.makeClass(Py.java:2060) at subprocess$py.f$0(C:/FIJI-W~1/Fiji.app/jars/jython-shaded-2.7.1.jar/Lib/subprocess.py:2013) at subprocess$py.call_function(C:/FIJI-W~1/Fiji.app/jars/jython-shaded-2.7.1.jar/Lib/subprocess.py) at org.python.core.PyTableCode.call(PyTableCode.java:171) at org.python.core.PyCode.call(PyCode.java:18) at org.python.core.imp.createFromCode(imp.java:436) at org.python.core.util.importer.importer_load_module(importer.java:116) at org.python.modules.zipimport.zipimporter.zipimporter_load_module(zipimporter.java:170) at org.python.modules.zipimport.zipimporter$zipimporter_load_module_exposer.call(Unknown Source) at org.python.core.PyBuiltinMethodNarrow.call(PyBuiltinMethodNarrow.java:46) at org.python.core.imp.loadFromLoader(imp.java:593) at org.python.core.imp.find_module(imp.java:547) at org.python.core.imp.import_next(imp.java:838) at org.python.core.imp.import_module_level(imp.java:957) at org.python.core.imp.importName(imp.java:1057) at org.python.core.ImportFunction.call(builtin.java:1280) at org.python.core.PyObject.call(PyObject.java:450) at org.python.core.builtin.import(builtin.java:1232) at org.python.core.imp.importOne(imp.java:1076) at cmtkgui$py.f$0(C:/FIJI-W~1/Fiji.app/plugins/CMTK_Registration/cmtkgui.py:372) at cmtkgui$py.call_function(C:/FIJI-W~1/Fiji.app/plugins/CMTK_Registration/cmtkgui.py) at org.python.core.PyTableCode.call(PyTableCode.java:171) at org.python.core.PyCode.call(PyCode.java:18) at org.python.core.imp.createFromCode(imp.java:436) at org.python.core.imp.createFromPyClass(imp.java:237) at org.python.core.imp.createFromPyClass(imp.java:205) at org.python.core.imp.loadFromSource(imp.java:657) at org.python.core.imp.find_module(imp.java:551) at org.python.core.imp.import_next(imp.java:838) at org.python.core.imp.import_module_level(imp.java:957) at org.python.core.imp.importName(imp.java:1057) at org.python.core.ImportFunction.call(builtin.java:1280) at org.python.core.PyObject.call(PyObject.java:450) at org.python.core.builtin.import(builtin.java:1232) at org.python.core.imp.importOne(imp.java:1076) at org.python.pycode._pyx0.f$0(CMTK_Registration/Install_CMTK.py:81) at org.python.pycode._pyx0.call_function(CMTK_Registration/Install_CMTK.py) at org.python.core.PyTableCode.call(PyTableCode.java:171) at org.python.core.PyCode.call(PyCode.java:18) at org.python.core.Py.runCode(Py.java:1614) at org.python.core.builtin.eval(builtin.java:497) at org.python.core.builtin.eval(builtin.java:501) at org.python.util.PythonInterpreter.eval(PythonInterpreter.java:259) at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:57) at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31) at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264) at org.scijava.script.ScriptModule.run(ScriptModule.java:160) at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66) at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: java.lang.UnsatisfiedLinkError: org.scijava.jython.shaded.com.kenai.jffi.Foreign.getVersion()I at org.scijava.jython.shaded.com.kenai.jffi.Foreign.newLoadError(Foreign.java:72) at org.scijava.jython.shaded.com.kenai.jffi.Foreign.access$300(Foreign.java:42) at org.scijava.jython.shaded.com.kenai.jffi.Foreign$InValidInstanceHolder.getForeign(Foreign.java:98) at org.scijava.jython.shaded.com.kenai.jffi.Foreign.getInstance(Foreign.java:103) at org.scijava.jython.shaded.com.kenai.jffi.Library.openLibrary(Library.java:157) at org.scijava.jython.shaded.com.kenai.jffi.Library.getCachedInstance(Library.java:131) at org.python.modules.jffi.DynamicLibrary.(DynamicLibrary.java:26) at org.python.modules.jffi.jffi.dlopen(jffi.java:43) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:497) at org.python.core.PyReflectedFunction.call(PyReflectedFunction.java:188) ... 84 more Caused by: java.lang.UnsatisfiedLinkError: org.scijava.jython.shaded.com.kenai.jffi.Foreign.getVersion()I at org.scijava.jython.shaded.com.kenai.jffi.Foreign.getVersion(Native Method) at org.scijava.jython.shaded.com.kenai.jffi.Foreign$InstanceHolder.getInstanceHolder(Foreign.java:53) at org.scijava.jython.shaded.com.kenai.jffi.Foreign$InstanceHolder.(Foreign.java:45) at org.scijava.jython.shaded.com.kenai.jffi.Foreign.getInstance(Foreign.java:103) at org.scijava.jython.shaded.com.kenai.jffi.Type$Builtin.lookupTypeInfo(Type.java:242) at org.scijava.jython.shaded.com.kenai.jffi.Type$Builtin.getTypeInfo(Type.java:237) at org.scijava.jython.shaded.com.kenai.jffi.Type.resolveSize(Type.java:155) at org.scijava.jython.shaded.com.kenai.jffi.Type.size(Type.java:138) at org.scijava.jython.shaded.jnr.ffi.provider.jffi.NativeRuntime$TypeDelegate.size(NativeRuntime.java:187) at org.scijava.jython.shaded.jnr.ffi.provider.AbstractRuntime.(AbstractRuntime.java:48) at org.scijava.jython.shaded.jnr.ffi.provider.jffi.NativeRuntime.(NativeRuntime.java:66) at org.scijava.jython.shaded.jnr.ffi.provider.jffi.NativeRuntime.(NativeRuntime.java:41) at org.scijava.jython.shaded.jnr.ffi.provider.jffi.NativeRuntime$SingletonHolder.(NativeRuntime.java:62) at org.scijava.jython.shaded.jnr.ffi.provider.jffi.NativeRuntime.getInstance(NativeRuntime.java:58) at org.scijava.jython.shaded.jnr.ffi.provider.jffi.Provider.(Provider.java:29) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:422) at java.lang.Class.newInstance(Class.java:442) at org.scijava.jython.shaded.jnr.ffi.provider.FFIProvider$SystemProviderSingletonHolder.getInstance(FFIProvider.java:68) at org.scijava.jython.shaded.jnr.ffi.provider.FFIProvider$SystemProviderSingletonHolder.(FFIProvider.java:57) at org.scijava.jython.shaded.jnr.ffi.provider.FFIProvider.getSystemProvider(FFIProvider.java:35) at org.scijava.jython.shaded.jnr.ffi.Library.loadLibrary(Library.java:114) at org.scijava.jython.shaded.jnr.posix.POSIXFactory$DefaultLibCProvider$SingletonHolder.(POSIXFactory.java:279) at org.scijava.jython.shaded.jnr.posix.POSIXFactory$DefaultLibCProvider.getLibC(POSIXFactory.java:283) at org.scijava.jython.shaded.jnr.posix.BaseNativePOSIX.(BaseNativePOSIX.java:37) at org.scijava.jython.shaded.jnr.posix.WindowsPOSIX.(WindowsPOSIX.java:132) at org.scijava.jython.shaded.jnr.posix.POSIXFactory.loadWindowsPOSIX(POSIXFactory.java:163) at org.scijava.jython.shaded.jnr.posix.POSIXFactory.loadNativePOSIX(POSIXFactory.java:136) at org.scijava.jython.shaded.jnr.posix.POSIXFactory.loadPOSIX(POSIXFactory.java:90) at org.scijava.jython.shaded.jnr.posix.LazyPOSIX.loadPOSIX(LazyPOSIX.java:38) at org.scijava.jython.shaded.jnr.posix.LazyPOSIX.posix(LazyPOSIX.java:32) at org.scijava.jython.shaded.jnr.posix.LazyPOSIX.isNative(LazyPOSIX.java:382) at org.python.modules.posix.PosixModule.classDictInit(PosixModule.java:131) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:497) at org.python.core.PyJavaType.init(PyJavaType.java:571) at org.python.core.PyType.createType(PyType.java:1523) at org.python.core.PyType.addFromClass(PyType.java:1462) at org.python.core.PyType.fromClass(PyType.java:1551) at org.python.core.imp.createFromClass(imp.java:469) at org.python.core.imp.loadBuiltin(imp.java:578) at org.python.core.imp.find_module(imp.java:534) at org.python.core.imp.import_next(imp.java:838) at org.python.core.imp.import_module_level(imp.java:957) at org.python.core.imp.importName(imp.java:1057) at org.python.core.ImportFunction.call(builtin.java:1280) at org.python.core.PyObject.call(PyObject.java:450) at org.python.core.builtin.import(builtin.java:1232) at org.python.core.imp.importAll(imp.java:1176) at os$py.f$0(C:/FIJI-W~1/Fiji.app/jars/jython-shaded-2.7.1.jar/Lib/os.py:726) at os$py.call_function(C:/FIJI-W~1/Fiji.app/jars/jython-shaded-2.7.1.jar/Lib/os.py) at org.python.core.PyTableCode.call(PyTableCode.java:171) at org.python.core.PyCode.call(PyCode.java:18) at org.python.core.imp.createFromCode(imp.java:436) at org.python.core.util.importer.importer_load_module(importer.java:116) at org.python.modules.zipimport.zipimporter.zipimporter_load_module(zipimporter.java:170) at org.python.modules.zipimport.zipimporter$zipimporter_load_module_exposer.call(Unknown Source) at org.python.core.PyBuiltinMethodNarrow.call(PyBuiltinMethodNarrow.java:46) at org.python.core.imp.loadFromLoader(imp.java:593) at org.python.core.imp.find_module(imp.java:547) at org.python.core.imp.import_next(imp.java:838) at org.python.core.imp.import_module_level(imp.java:957) at org.python.core.imp.importName(imp.java:1057) at org.python.core.ImportFunction.call(builtin.java:1280) at org.python.core.PyObject.call(PyObject.java:450) at org.python.core.builtin.import(builtin.java:1232) at org.python.core.imp.importOne(imp.java:1076) at site$py.f$0(C:/FIJI-W~1/Fiji.app/jars/jython-shaded-2.7.1.jar/Lib/site.py:637) at site$py.call_function(C:/FIJI-W~1/Fiji.app/jars/jython-shaded-2.7.1.jar/Lib/site.py) at org.python.core.PyTableCode.call(PyTableCode.java:171) at org.python.core.PyCode.call(PyCode.java:18) at org.python.core.imp.createFromCode(imp.java:436) at org.python.core.util.importer.importer_load_module(importer.java:116) at org.python.modules.zipimport.zipimporter.zipimporter_load_module(zipimporter.java:170) at org.python.modules.zipimport.zipimporter$zipimporter_load_module_exposer.call(Unknown Source) at org.python.core.PyBuiltinMethodNarrow.call(PyBuiltinMethodNarrow.java:46) at org.python.core.imp.loadFromLoader(imp.java:593) at org.python.core.imp.find_module(imp.java:547) at org.python.core.imp.import_next(imp.java:838) at org.python.core.imp.import_first(imp.java:863) at org.python.core.imp.load(imp.java:721) at org.python.core.Py.importSiteIfSelected(Py.java:1795) at org.python.util.PythonInterpreter.(PythonInterpreter.java:116) at org.python.util.PythonInterpreter.threadLocalStateInterpreter(PythonInterpreter.java:81) at org.python.jsr223.PyScriptEngine.(PyScriptEngine.java:27) at org.python.jsr223.PyScriptEngineFactory.getScriptEngine(PyScriptEngineFactory.java:85) at org.scijava.script.AdaptedScriptLanguage.getScriptEngine(AdaptedScriptLanguage.java:140) at org.scijava.script.ScriptModule.getEngine(ScriptModule.java:108) at org.scijava.script.ScriptModule.run(ScriptModule.java:129) ... 8 more

MaximilianHoffmann commented 5 years ago

I experience the same error on windows

uherget commented 5 years ago

Same here. I solved the first error (java.nio.charset.UnsupportedCharsetException: cp0) by launching Fiji with the parameter "-Dpython.console.encoding=UTF-8", but I can't find any solution for the other one (java.lang.UnsatisfiedLinkError: org.scijava.jython.shaded.com.kenai.jffi.Foreign.getVersion()I).