users > Trouble running munger on Mac
Showing 1-8 of 8 posts
Reply
Display:
Results per page:
Apr 27, 2020  04:04 PM | Nicholas Santistevan - University of Wisconsin - Madison
Trouble running munger on Mac
I am doing some image registration in FIJI and am attempting to use the Jefferis CMTK Registration GUI.

In my hands, this plugin successfully creates a command file, but when I try to run the munger command file, I am getting an error that states that I do not have appropriate access privileges. I've checked and I have read and write capabilities as the admin of my computer. I've tried restarting the computer, and uninstalling and reinstalling the plugin but I am still getting this error.

Any help figuring out how to get this plugin to work would be greatly appreciated.
Attachment: Screen Shot 2020-04-13 at 4.54.44 PM.png
Quote & Reply Reply 
Apr 27, 2020  05:04 PM | Greg Jefferis
Trouble running munger on Mac
Dear Nicholas,

What is your OS? Do you want to post your script?

Best,

Greg Jefferis.

Quote & Reply Reply 
Apr 27, 2020  08:04 PM | Nicholas Santistevan - University of Wisconsin - Madison
RE: Trouble running munger on Mac
Hello, 

I've tried it on two Macs, one a MacOS High Sierra and one a MacOS Mojave. 

My script is: 

INFO] Reading available sites from https://imagej.net/
bindir is /Applications/Fiji.app/bin/cmtk
munger is /Applications/Fiji.app/bin/cmtk/munger
Jefferis, Potter 2007
Chosen reg params: Cachero, Ostrovsky 2010
/Users/marcwolman/Desktop/cacna2d3_sa16189/Registration/Feb2020-cacna2d3sa16189/refbrain//Ref20131120pt14pl2.nrrd
refbrain/Ref20131120pt14pl2.nrrd
Cachero, Ostrovsky 2010
"/Applications/Fiji.app/bin/cmtk/munger" -b "/Applications/Fiji.app/bin/cmtk" -a -w -r 0102 – -awr 0102 -X 52 -C 8 -G 80 -R 3 -A '—accuracy 0.4' -W '—accuracy 1.6' -T 4 -s "refbrain/Ref20131120pt14pl2.nrrd" images

It gives me the following Error message in FIJI:

[ERROR] Traceback (most recent call last):
File "CMTK_Registration/CMTK_Registration_GUI.py", line 211, in
File "CMTK_Registration/CMTK_Registration_GUI.py", line 211, in
File "__pyclasspath__/cmtkgui$py.class", line 95, in makescript
UnicodeEncodeError: 'ascii' codec can't encode character u'\u2013' in position 210: ordinal not in range(128)

at org.python.core.codecs.strict_errors(codecs.java:208)
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:498)
at org.python.core.JavaFunc.__call__(Py.java:3026)
at org.python.core.PyObject.__call__(PyObject.java:450)
at org.python.core.codecs.encoding_error(codecs.java:1538)
at org.python.core.codecs.PyUnicode_EncodeIntLimited(codecs.java:1211)
at org.python.core.codecs.PyUnicode_EncodeASCII(codecs.java:1170)
at org.python.core.codecs.encode(codecs.java:165)
at org.python.core.PyString.encode(PyString.java:3981)
at org.python.core.PyFile.asWritable(PyFile.java:490)
at org.python.core.PyFile.file_write(PyFile.java:450)
at org.python.core.PyFile$file_write_exposer.__call__(Unknown Source)
at org.python.core.PyObject.__call__(PyObject.java:484)
at cmtkgui$py.makescript$7(/Applications/Fiji.app/plugins/CMTK_Registration/cmtkgui.py:98)
at cmtkgui$py.call_function(/Applications/Fiji.app/plugins/CMTK_Registration/cmtkgui.py)
at org.python.core.PyTableCode.call(PyTableCode.java:171)
at org.python.core.PyBaseCode.call(PyBaseCode.java:308)
at org.python.core.PyFunction.function___call__(PyFunction.java:471)
at org.python.core.PyFunction.__call__(PyFunction.java:466)
at org.python.pycode._pyx0.f$0(CMTK_Registration/CMTK_Registration_GUI.py:219)
at org.python.pycode._pyx0.call_function(CMTK_Registration/CMTK_Registration_GUI.py)
at org.python.core.PyTableCode.call(PyTableCode.java:171)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1614)
at org.python.core.__builtin__.eval(__builtin__.java:497)
at org.python.core.__builtin__.eval(__builtin__.java:501)
at org.python.util.PythonInterpreter.eval(PythonInterpreter.java:259)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:57)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at org.scijava.script.ScriptModule.run(ScriptModule.java:160)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

Thank you for your time, 
Nik
Attachment: Screen Shot 2020-04-27 at 2.34.41 PM.png
Quote & Reply Reply 
May 6, 2020  06:05 PM | Nicholas Santistevan - University of Wisconsin - Madison
RE: Trouble running munger on Mac
Hello,

I'm just following up to see if there was an identifiable problem with my script?

Thanks,
Nik 

Originally posted by Nicholas Santistevan:
Hello, 

I've tried it on two Macs, one a MacOS High Sierra and one a MacOS Mojave. 

My script is: 

INFO] Reading available sites from https://imagej.net/
bindir is /Applications/Fiji.app/bin/cmtk
munger is /Applications/Fiji.app/bin/cmtk/munger
Jefferis, Potter 2007
Chosen reg params: Cachero, Ostrovsky 2010
/Users/marcwolman/Desktop/cacna2d3_sa16189/Registration/Feb2020-cacna2d3sa16189/refbrain//Ref20131120pt14pl2.nrrd
refbrain/Ref20131120pt14pl2.nrrd
Cachero, Ostrovsky 2010
"/Applications/Fiji.app/bin/cmtk/munger" -b "/Applications/Fiji.app/bin/cmtk" -a -w -r 0102 – -awr 0102 -X 52 -C 8 -G 80 -R 3 -A '—accuracy 0.4' -W '—accuracy 1.6' -T 4 -s "refbrain/Ref20131120pt14pl2.nrrd" images

It gives me the following Error message in FIJI:

[ERROR] Traceback (most recent call last):
File "CMTK_Registration/CMTK_Registration_GUI.py", line 211, in
File "CMTK_Registration/CMTK_Registration_GUI.py", line 211, in
File "__pyclasspath__/cmtkgui$py.class", line 95, in makescript
UnicodeEncodeError: 'ascii' codec can't encode character u'\u2013' in position 210: ordinal not in range(128)

at org.python.core.codecs.strict_errors(codecs.java:208)
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:498)
at org.python.core.JavaFunc.__call__(Py.java:3026)
at org.python.core.PyObject.__call__(PyObject.java:450)
at org.python.core.codecs.encoding_error(codecs.java:1538)
at org.python.core.codecs.PyUnicode_EncodeIntLimited(codecs.java:1211)
at org.python.core.codecs.PyUnicode_EncodeASCII(codecs.java:1170)
at org.python.core.codecs.encode(codecs.java:165)
at org.python.core.PyString.encode(PyString.java:3981)
at org.python.core.PyFile.asWritable(PyFile.java:490)
at org.python.core.PyFile.file_write(PyFile.java:450)
at org.python.core.PyFile$file_write_exposer.__call__(Unknown Source)
at org.python.core.PyObject.__call__(PyObject.java:484)
at cmtkgui$py.makescript$7(/Applications/Fiji.app/plugins/CMTK_Registration/cmtkgui.py:98)
at cmtkgui$py.call_function(/Applications/Fiji.app/plugins/CMTK_Registration/cmtkgui.py)
at org.python.core.PyTableCode.call(PyTableCode.java:171)
at org.python.core.PyBaseCode.call(PyBaseCode.java:308)
at org.python.core.PyFunction.function___call__(PyFunction.java:471)
at org.python.core.PyFunction.__call__(PyFunction.java:466)
at org.python.pycode._pyx0.f$0(CMTK_Registration/CMTK_Registration_GUI.py:219)
at org.python.pycode._pyx0.call_function(CMTK_Registration/CMTK_Registration_GUI.py)
at org.python.core.PyTableCode.call(PyTableCode.java:171)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1614)
at org.python.core.__builtin__.eval(__builtin__.java:497)
at org.python.core.__builtin__.eval(__builtin__.java:501)
at org.python.util.PythonInterpreter.eval(PythonInterpreter.java:259)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:57)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at org.scijava.script.ScriptModule.run(ScriptModule.java:160)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

Thank you for your time, 
Nik
Quote & Reply Reply 
May 6, 2020  06:05 PM | Greg Jefferis
RE: Trouble running munger on Mac
Hi Nik,

Can you post the actual .command file?

You previously posted something that looked like the ImageJ log.

Best,

Greg.
Quote & Reply Reply 
May 6, 2020  06:05 PM | Greg Jefferis
RE: Trouble running munger on Mac
Also with respect to the image you sent about a permissions issue, can you go to the folder containing your script in the Terminal and do:

cd /some/folder/ # CHANGE TO CORRECT PATH

ls -l

chmod a+x *.command

Finally can you confirm if your account has admin privileges?

Best,

Greg.
Quote & Reply Reply 
May 14, 2020  03:05 PM | Nicholas Santistevan - University of Wisconsin - Madison
RE: Trouble running munger on Mac
Hello,

Thank you for the suggestion for changing permissions on the folder. This worked.  I've determined the problem I was having with the GUI not functioning properly. I had entered content into the "(Further) Registration Params" field of the CMTK Registration GUI but inadvertently had entered a long — instead of a double --. Changing it back to -- fixed the issue and I was able to run it.

Thank you for your time and help,
Nik Santistevan
Quote & Reply Reply 
May 14, 2020  03:05 PM | Greg Jefferis
RE: Trouble running munger on Mac
Dear Nik, I'm glad to hear that everything is working for you now – thanks for sharing your fixes. Unfortunately -- is often autoconverted to an em dash –. Best, Greg.
Quote & Reply Reply 
Reply