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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>>>>> >
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>>>>>
>>>>>
>>>>
>>>
>>>
>>
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>
>
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