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 <abri...@gmail.com> 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 <abri...@gmail.com>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 <abri...@gmail.com>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 <abri...@gmail.com>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 <luca.ant...@orobix.com>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
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>>>>>
>>>>>
>>>>
>>>
>>
>
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