Hi Luca,
Thanks for the suggestion. By looking through the file, I realized what my
mistake was. The script requires the centerline files to be in their own
folder in the specified directory path, which in this case is C:\Program
Files (x86)\vmtk\Install\bin\id1, but I had them in C:\Program Files
(x86)\vmtk\Install\bin.
On Mon, May 6, 2013 at 11:36 PM, Luca Antiga <luca.ant...@gmail.com> wrote:
> 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 vmtkmodules
>>>> ("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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>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
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>>>>
>>>
>>>
>>
> <vtkoutputwindowerror.JPG>
>
>
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