Re: [vmtk-users] Command line parameters for vmtkLevelSetSegmentation
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lucantiga
From: Richard A. <ab...@gm...> - 2013-06-26 21:54:26
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Answering my own question again: It turns out that the Colliding Fronts initialization code didn't support multiple start and end points. Lines 295-296: seedIds1.InsertNextId(self.Image.ComputePointId([self.SourcePoints[0],self.SourcePoints[1],self.SourcePoints[2]])) seedIds2.InsertNextId(self.Image.ComputePointId([self.TargetPoints[0],self.TargetPoints[1],self.TargetPoints[2]])) Need to be replaced with: for i in range(len(self.SourcePoints)/3): seedIds1.InsertNextId(self.Image.ComputePointId([self.SourcePoints[3*i+0],self.SourcePoints[3*i+1],self.SourcePoints[3*i+2]])) for i in range(len(self.TargetPoints)/3): seedIds2.InsertNextId(self.Image.ComputePointId([self.TargetPoints[3*i+0],self.TargetPoints[3*i+1],self.TargetPoints[3*i+2]])) Now it works. On Wed, Jun 26, 2013 at 5:12 PM, Richard Abrich <ab...@gm...> wrote: > Sorry for the deluge of emails. I wasn't able to successfully get the > latest version of the VMTK source to run properly, so instead I just > downloaded the latest version of vmtkImageInitialization.py, which accepts > the parameters you specified. > > My question is this: the description for the SourcePoints parameter is > "list of source point IJK coordinates". Am I able to specify more than one > SourcePoint and TargetPoint, and have it iterate over them? The alternative > would be to save the results to disk after each call and then merge them > all at the end before performing the LevelSetSegmentation, which seems > pretty hacky. > > > > On Wed, Jun 26, 2013 at 11:07 AM, Richard Abrich <ab...@gm...>wrote: > >> Hi again, >> >> I noticed that the latest version of VMTK in the Github repo has those >> parameters you specified. I'm currently compiling it, and will let you know >> how it goes. >> >> Thanks, >> Richard >> >> >> >> On Tue, Jun 25, 2013 at 5:37 PM, Richard Abrich <ab...@gm...>wrote: >> >>> Hi Luca, >>> >>> Sorry I forgot to CC my last email to the mailing list. >>> >>> A couple of addendums to my previous email (below): >>> >>> 1) I converted my data to the .mha format and am using the exact command >>> you suggested. >>> >>> 2) I used vmtk-exe.pyc instead of vmtk-exe.pyw in order to view the >>> output. The relevant lines seem to be: >>> >>> Parsing options vmtkimageinitialization >>> vmtkimageinitialization error: unknown option -interactive >>> >>> Just FYI, here is the revision information in the >>> vmtkimageinitialization.py script: >>> >>> ## Date: $Date: 2006/05/31 10:51:21 $ >>> ## Version: $Revision: 1.19 $ >>> >>> Is there a newer version I can grab from somewhere? >>> >>> >>> On Tue, Jun 25, 2013 at 5:13 PM, Richard Abrich <ab...@gm...>wrote: >>> >>>> Hi Luca, >>>> >>>> Thanks so much for your help. I have a couple of questions: >>>> >>>> 1) My data isn't .mha format, but rather stored as a dicom set. I tried >>>> to do something like this instead: >>>> >>>> vmtkimagereader -f dicom -d C:/DICOM --pipe vmtkimageinitialization >>>> -interactive 0 -method collidingfronts -lowerthreshold 200.0 -sourcepoints >>>> 54 25 12 -targetpoints 89 60 24 --pipe vmtklevelsetsegmentation -iterations >>>> 200 -advection 1.0 -curvature 0.1 -propagation 0.0 -ofile C:/out.vtk >>>> >>>> However, the output file wasn't written, and I'm not sure how to check >>>> whether anything happened. >>>> >>>> 2) On a related note, I notice that in your example, you specify the >>>> ifile parameter for vmtklevelsetsegmentation again, even though you are >>>> piping the results from vmtkimageinitialization. Is this necessary? How can >>>> I do this using dicom sets instead? >>>> >>>> 3) A few of the parameters you specify for vmtkimagereader (e.g. >>>> interactive, method, lowerthreshold, sourcepoints, targetpoints) aren't >>>> listed in the documentation at >>>> http://www.vmtk.org/VmtkScripts/vmtkimageinitialization/ . I can see >>>> that LowerThreshold and UpperThreshold are properties of the >>>> vmtkImageInitialization object in vmtkImageInitialization.py, but the other >>>> parameters are a mystery. Where can I read more about them? >>>> >>>> Thanks again, >>>> Richard >>>> >>>> >>>> On Thu, Jun 20, 2013 at 4:41 PM, Luca Antiga <luc...@or...>wrote: >>>> >>>>> Hi Richard, >>>>> indeed there is a way. The initialization phase in >>>>> vmtklevelsetsegmentation is performed by vmtkimageinitialization, >>>>> which accepts parameters at the command line and whose output can be >>>>> piped to vmtklevelsetsegmentation (in which >>>>> case the latter will use the initialized level sets generated by the >>>>> former). vmtklevelsetsegmentation can also run >>>>> non-interactively by specifying iterations and evolution parameters at >>>>> the command line. Here's a sample pipe: >>>>> >>>>> vmtkimageinitialization -ifile your_image_file.mha -interactive 0 >>>>> -method collidingfronts -lowerthreshold 200.0 -sourcepoints 54 25 12 >>>>> -targetpoints 89 60 24 --pipe vmtklevelsetsegmentation -ifile >>>>> you_image_file.mha -iterations 500 -advection 1.0 -curvature 0.1 >>>>> -propagation 0.0 -ofile level_set_file.mha >>>>> >>>>> One caveat: sourcepoints and targetpoints are in IJK coordinates (i.e. >>>>> voxel indices), not physical coordinates. >>>>> >>>>> Hope this helps, >>>>> >>>>> >>>>> Luca >>>>> >>>>> >>>>> On Jun 18, 2013, at 10:51 PM, Richard Abrich wrote: >>>>> >>>>> Hello, >>>>> >>>>> I'm interested in calling vmtkLevelSetSegmentation from a script. I >>>>> want to run colliding fronts with arbitrary thresholds and start/end >>>>> position vectors for the initial segmentation, and then run the level set >>>>> segmentation with arbitrary parameters. >>>>> >>>>> Unfortunately, there doesn't seem to be any way to specify these >>>>> parameters from the command line. What might be the easiest way to >>>>> accomplish this? >>>>> >>>>> Thanks, >>>>> Richard >>>>> ------------------------------------------------------------------------------ >>>>> This SF.net email is sponsored by Windows: >>>>> >>>>> Build for Windows Store. >>>>> >>>>> >>>>> http://p.sf.net/sfu/windows-dev2dev_______________________________________________ >>>>> vmtk-users mailing list >>>>> vmt...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users >>>>> >>>>> >>>>> >>>> >>> >> > |