Re: [vmtk-users] vmtkApps?
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From: Evan K. <to...@gm...> - 2013-05-07 07:59:01
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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 <luc...@gm...> 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 <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 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 <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 >>>>>>> > >>>>>>> ------------------------------------------------------------------------------ >>>>>>> > Precog is a next-generation analytics platform capable of advanced >>>>>>> > analytics on semi-structured data. The platform includes APIs for >>>>>>> building >>>>>>> > apps and a phenomenal toolset for data science. Developers can use >>>>>>> > our toolset for easy data analysis & visualization. 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