jefferis
commented
4 years ago Hi @fvanzi as you have seen, there are complications with CMTK on windows and unfortunately I do not develop or test there. My previous recommendation was to install CMTK via cygwin but recently people have had success using the Windows Subsystem for Linux (WSL). See https://www.nitrc.org/forum/message.php?msg_id=29012. You would not be able to use this CMTK installation directly with the CMTK GUI, but you could edit the script files produced by CMTK gui to use that.
fvanzi
Hi, I am new to the forum so my apologies if I repeat something from previous posts. I have read all threads but could not find a solution to my problem. On PC, widnows10, I am trying to install CMTK following the instructions in: https://github.com/jefferis/fiji-cmtk-gui
When I select "Install CMTK" in plugins->CMTK Registration I get the following message: console: Failed to install '': java.nio.charset.UnsupportedCharsetException: cp0. [ERROR] Traceback (most recent call last): File "fiji-cmtk-gui-0.1.1/fiji-cmtk-gui-0.1.1/Install_CMTK.py", line 11, in
File "C:\PROGRA~1\FIJI-W~1\Fiji.app\plugins\CMTK_Registration\cmtkgui.py", line 5, in
import subprocess, re, urllib2, tempfile
File "C:\PROGRA~1\FIJI-W~1\Fiji.app\jars\jython-shaded-2.7.1.jar\Lib\subprocess.py", line 799, in
File "C:\PROGRA~1\FIJI-W~1\Fiji.app\jars\jython-shaded-2.7.1.jar\Lib\subprocess.py", line 1399, in Popen
File "C:\PROGRA~1\FIJI-W~1\Fiji.app\jars\jython-shaded-2.7.1.jar\Lib\ctypes__init.py", line 281, in getattr
File "C:\PROGRA~1\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
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$0(C:/PROGRA~1/FIJI-W~1/Fiji.app/jars/jython-shaded-2.7.1.jar/Lib/os.py:726)
at os$py.call_function(C:/PROGRA~1/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$0(C:/PROGRA~1/FIJI-W~1/Fiji.app/jars/jython-shaded-2.7.1.jar/Lib/site.py:637)
at site$py.call_function(C:/PROGRA~1/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
I have seen something like this mentioned by others but could not find a solution posted by anyone. Any help will be greatly appreciated! Thanks!! Francesco