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 <tos...@gmail.com> 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 <tos...@gmail.com> 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 <luca.ant...@orobix.com> 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 <luca.ant...@orobix.com> 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 <luca.ant...@orobix.com>
>>>>>> 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 <tos...@gmail.com> wrote:
>>>>>>>>> Hi Luca,
>>>>>>>>>
>>>>>>>>> Thanks for the info.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Mon, Apr 22, 2013 at 7:01 AM, Luca Antiga <luca.ant...@orobix.com>
>>>>>>>>> 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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