Hi,


I'm having an issue installing the CMTK gui from Fiji on a machine running windows 7.  When selecting to install the gui, I get the following error message in the console (with no subsequent installation of the plugin):

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.app\plugins\CMTK_Registration\cmtkgui.py", line 5, in
import subprocess, re, urllib2, tempfile
File "C:\Fiji.app\jars\jython-shaded-2.7.1.jar\Lib\subprocess.py", line 799, in
File "C:\Fiji.app\jars\jython-shaded-2.7.1.jar\Lib\subprocess.py", line 1399, in Popen
File "C:\Fiji.app\jars\jython-shaded-2.7.1.jar\Lib\ctypes\__init__.py", line 281, in __getattr__
File "C:\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__$49(C:/Fiji.app/jars/jython-shaded-2.7.1.jar/Lib/ctypes/__init__.py:262)
at ctypes$py.call_function(C:/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__$54(C:/Fiji.app/jars/jython-shaded-2.7.1.jar/Lib/ctypes/__init__.py:283)
at ctypes$py.call_function(C:/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$22(C:/Fiji.app/jars/jython-shaded-2.7.1.jar/Lib/subprocess.py:1886)
at subprocess$py.call_function(C:/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$0(C:/Fiji.app/jars/jython-shaded-2.7.1.jar/Lib/subprocess.py:2013)
at subprocess$py.call_function(C:/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$0(C:/Fiji.app/plugins/CMTK_Registration/cmtkgui.py:372)
at cmtkgui$py.call_function(C:/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$0(C:/Fiji.app/jars/jython-shaded-2.7.1.jar/Lib/os.py:726)
at os$py.call_function(C:/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$0(C:/Fiji.app/jars/jython-shaded-2.7.1.jar/Lib/site.py:637)
at site$py.call_function(C:/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

Any ideas on what the issue might be?

Thanks!

I’m sorry I missed this earlier. It looks similar to the following issue caused by changes in Fiji

https://forum.image.sc/t/fiji-with-pytho...

Perhaps you could try the fix they mention. Best,
Greg.

Dear Greg,
I've followed the step-by-step instruction on https://github.com/jefferis/fiji-cmtk-gui 

to install the CMTK GUI plugin on a 10.15.7 Mac OS X  with clean installs of Fiji. I installed Fiji, downloaded the CMTK GUI zip, expanded it, renamed it to CMTK_Registration, moved it to the plugins/Scripts/Plugins folder, and restarted Fiji. While CMTK_Registration appeared in the Fiji Plugin menu [1] - image attached, clicking one of the options, such as "Install CMTK" or "Update to development CMTK  GUI" gave me this error message on the console [2].

[2]
[ERROR] Traceback (most recent call last):
File "Install_CMTK.py", line 11, in
ImportError: No module named cmtkgui

at org.python.core.Py.ImportError(Py.java:329)
at org.python.core.imp.import_first(imp.java:1230)
at org.python.core.imp.import_module_level(imp.java:1361)
at org.python.core.imp.importName(imp.java:1528)
at org.python.core.ImportFunction.__call__(__builtin__.java:1285)
at org.python.core.PyObject.__call__(PyObject.java:433)
at org.python.core.__builtin__.__import__(__builtin__.java:1232)
at org.python.core.imp.importOne(imp.java:1547)
at org.python.pycode._pyx1.f$0(Install_CMTK.py:81)
at org.python.pycode._pyx1.call_function(Install_CMTK.py)
at org.python.core.PyTableCode.call(PyTableCode.java:173)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1687)
at org.python.core.__builtin__.eval(__builtin__.java:497)
at org.python.core.__builtin__.eval(__builtin__.java:501)
at org.python.util.PythonInterpreter.eval(PythonInterpreter.java:255)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:57)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at org.scijava.script.ScriptModule.run(ScriptModule.java:157)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)



I tried moving cmtkgui.py helper script out of the CMTK_registration folder as recommended by erichamc https://github.com/jefferis/fiji-cmtk-gui/issues/1. Restarted Fiji> Install CMTK. It doesn't seems to fix the problem.

Any other recommendation?

Caroline

Dear Caroline, sorry you’re having trouble but that doesn’t sound like the recommended install procedure. Did you try following the steps in the readme using the Fiji update site?

https://github.com/jefferis/fiji-cmtk-gu...

Iirc if you are going to install manually you need to ensure that jython compiles the py file and it ends up in the class path. I forget the details but can look into it if there’s a reason why the update site won’t work for you.

All the best,

Greg.