Re: [vmtk-users] vmtkApps?

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Hi Evan,
 really hard to infer anything. Do you have any indication of where it's crashing? Like after centerlines, or before...
You could place a few print statements along the python file you're running, just to have an idea of where it's failing. 

Luca

On 07/mag/2013, at 00:47, Evan Kao <to...@gm...> wrote:

> Hi Luca,
> 
> The function seems to import the modules fine for now, but for whatever reason, it keeps crashing when I actually try to use it.  I am only following the tutorial (pretty much just copying and pasting commands), so this might just be a problem with using Win XP 64-bit.
> 
> The command line interface output gives:
> USAGE:
>       ./patchandinterpolatecenterlines.py inputfilesDirectory caseID aneurysmType
> 
> Inputfiles Directory    C:\Program Files (x86)\vmtk\Install\bin
> case ID            id1
> Aneurysm Type        lateral
> 
> Then a vtkOutputWindow pops up with an error, which is shortly followed by a python crash message.  Unfortunately, I can't seem to scroll through the vtkOutputWindow because it freezes up, so the error information is limited only to the screenshot I took (attached).  Is there anything you can glean from this?
> 
> Thanks,
> Evan Kao
> 
> 
> On Mon, May 6, 2013 at 2:02 PM, Evan Kao <to...@gm...> wrote:
>> Hi Luca,
>> 
>> I added the environmental variables, and got the error:
>> 
>> File "patandinterpcl.py", line 369, in <module>
>>    inputfiledirectory = sys.argv[1]
>> IndexError: list index out of range
>> 
>> Since I didn't enter any input arguments, I'm guessing this is supposed to happen.  I'll try to use it with some files now.
>> 
>> Thanks,
>> Evan Kao
>> 
>> 
>> On Mon, May 6, 2013 at 1:36 PM, Luca Antiga <luc...@or...> wrote:
>>> Hi Evan,
>>>  ok, I see. Try with the following and please report the eventual error you get.
>>> 
>>> PATH
>>>   C:\"Program Files (x86)"\vmtk\Install\bin;
>>>   C:\"Program Files (x86)"\vmtk\Install\lib;
>>>   C:\"Program Files (x86)"\vmtk\Install\lib\vtk-5.8;
>>>   C:\"Program Files (x86)"\vmtk\Install\lib\vmtk;
>>>   C:\"Program Files (x86)"\vmtk\Install\bin\Python;
>>> PYTHONPATH
>>>   C:\"Program Files (x86)"\vmtk\Install\lib\vmtk;
>>>   C:\"Program Files (x86)"\vmtk\Install\bin\Python;
>>>   C:\"Program Files (x86)"\vmtk\Install\lib\vtk-5.8;
>>> 
>>> Luca
>>> 
>>> 
>>> On May 6, 2013, at 9:28 PM, Evan Kao wrote:
>>> 
>>>> Hello Luca, 
>>>> 
>>>> I tried the batch file, but it didn't work.  I think "set" in Win XP only allows temporary changes to environmental variables.  I can however use My Computer > System Properties > Advanced > Environmental Variables to modify PATH permanently and create a new variable PYTHONPATH.  But some of the directories you gave didn't match up to what was installed.  Here are the list of directories in vmtk on my machine:
>>>> 
>>>> C:\Program Files (x86)\vmtk\icon
>>>> C:\Program Files (x86)\vmtk\Install
>>>> C:\Program Files (x86)\vmtk\Install\bin
>>>> C:\Program Files (x86)\vmtk\Install\lib
>>>> C:\Program Files (x86)\vmtk\Install\bin\Python
>>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk
>>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\gtk
>>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\qt
>>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\qt4
>>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\test
>>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\tk
>>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\util
>>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\wx
>>>> C:\Program Files (x86)\vmtk\Install\lib\vmtk
>>>> C:\Program Files (x86)\vmtk\Install\lib\vtk-5.8
>>>> C:\Program Files (x86)\vmtk\Install\lib\vmtk\vmtk
>>>> 
>>>> I can make guesses on a few, but not all (like site-packages or InsightToolkit).
>>>> 
>>>> Thanks,
>>>> Evan Kao
>>>> 
>>>> 
>>>> On Mon, May 6, 2013 at 5:44 AM, Luca Antiga <luc...@or...> wrote:
>>>>> Hi Evan,
>>>>>  it's an environment variables issue and yes, it's currently not nice to run vmtkApps in Windows, sorry about this.
>>>>> 
>>>>> What you can do is create a patchanterinterpolatecenterlines.bat file (the name is irrelevant, the important is the .bat extension) with the following content:
>>>>> 
>>>>> set VMTK_DIR=C:\"Program Files (x86)"\vmtk
>>>>> set PATH=%VMTK_DIR%bin;%VMTK_DIR%lib\InsightToolkit;%VMTK_DIR%lib\Python;%PATH%
>>>>> set PYTHONPATH=%VMTK_DIR%lib\site-packages;%VMTK_DIR%lib\vtk-5.6;%VMTK_DIR%lib\vmtk
>>>>> cd %VMTK_DIR%
>>>>> python patchanterinterpolatecenterlines.py
>>>>> 
>>>>> Then double click on the .bat file. Let me know if this works or what error messages it produces.
>>>>> 
>>>>> We'll have to think about a nicer solution than this in the future.
>>>>> 
>>>>> 
>>>>> Luca
>>>>> 
>>>>> 
>>>>> On May 2, 2013, at 10:04 PM, Evan Kao wrote:
>>>>> 
>>>>>> Hi Luca, 
>>>>>> 
>>>>>>> You can move the files (you just need the files in vmtkApps/CerebralAneurysms/ParentVesselReconstruction) into any directory. 
>>>>>>> The you should invoke the scripts at the command line, but in order to do this you need Windows to "see" python and the vmtk modules.
>>>>>>> What are the directories where Python and vmtk are installed on our machine?
>>>>>> 
>>>>>> Both vmtk and Python are in their default directories (Python was installed through vmtk):
>>>>>> 
>>>>>> C:\Program Files (x86)\vmtk
>>>>>> C:\Python27
>>>>>> 
>>>>>> It seems I was able to open patchanterinterpolatecenterlin
>>>>>> es.py in the command line interface, but it doesn't see the vmtk modules ("Import Error: no module named vtk").  How can I remedy this?
>>>>>> 
>>>>>> Thanks,
>>>>>> Evan Kao
>>>>>> 
>>>>>> 
>>>>>> On Wed, May 1, 2013 at 5:30 AM, Luca Antiga <luc...@or...> wrote:
>>>>>>> Hi Evan,
>>>>>>> 
>>>>>>> On Apr 26, 2013, at 8:39 AM, Evan Kao wrote:
>>>>>>> 
>>>>>>>> Hi Luca,
>>>>>>>> 
>>>>>>>> I had some questions on using the Python scripts (having little Python experience):
>>>>>>>> 
>>>>>>>> 1.  Into which directory should I move the files (in Windows; files obtained from the source file zip)?
>>>>>>> 
>>>>>>> You can move the files (you just need the files in vmtkApps/CerebralAneurysms/ParentVesselReconstruction) into any directory. 
>>>>>>> The you should invoke the scripts at the command line, but in order to do this you need Windows to "see" python and the vmtk modules.
>>>>>>> What are the directories where Python and vmtk are installed on our machine?
>>>>>>> 
>>>>>>>> 2.  I was confused by the form of the command "python patchandinterpolatecenterline.py directoryPath id1 lateral" from the tutorial.  Are we supposed to call these functions from the command line/Python shell or can we still do it inside vmtk?
>>>>>>> 
>>>>>>> They are meant to be run outside of vmtk, at the command line.
>>>>>>> 
>>>>>>> Luca
>>>>>>> 
>>>>>>>> Thanks for the help,
>>>>>>>> Evan Kao
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> On Mon, Apr 22, 2013 at 11:03 AM, Evan Kao <to...@gm...> wrote:
>>>>>>>>> Hi Luca,
>>>>>>>>> 
>>>>>>>>> Thanks for the info.
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> On Mon, Apr 22, 2013 at 7:01 AM, Luca Antiga <luc...@or...> wrote:
>>>>>>>>>> Hello Evan,
>>>>>>>>>>  at the present stage you can download them from github.com/vmtk/vmtk
>>>>>>>>>> 
>>>>>>>>>> If you don't use git, just get the source code zip at
>>>>>>>>>> 
>>>>>>>>>> https://github.com/vmtk/vmtk/archive/master.zip
>>>>>>>>>> 
>>>>>>>>>> and unpack. vmtkApps contains the Python scripts you're looking for.
>>>>>>>>>> 
>>>>>>>>>> Best,
>>>>>>>>>> 
>>>>>>>>>> Luca
>>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>> On Apr 20, 2013, at 12:09 AM, Evan Kao wrote:
>>>>>>>>>> 
>>>>>>>>>> > Hello vmtk-users,
>>>>>>>>>> >
>>>>>>>>>> > I'm interested in going through the parent vessel reconstruction tutorial but I don't think I have the relevant Python scripts.  The tutorial says the files are in the vmtkApps folder, but I couldn't find anything like that.  Are they usually included in the installation?  Where could I find these scripts (and possibly other vmtkApps)?
>>>>>>>>>> >
>>>>>>>>>> > Thank you,
>>>>>>>>>> > Evan Kao
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> 
> <vtkoutputwindowerror.JPG>
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