Hi Gael,
Thank for your response. It is working correctly.
Now I would like to do the same thing but with N regions and each region of
different label.
How can I do that ? Do I need to create a loop to extract every region ?
Example :
for i in xrange(im.max()+1):
connect_ = tvtk.PolyDataConnectivityFilter(extraction_mode=6,
closest_point=ndimage.center_of_mass(im
== i))
connect = mlab.pipeline.user_defined(contour, filter=connect_)
surf = mlab.pipeline.surface(connect,color=(0.9, 0.72, 0.62))
It is quite slow to compute this code.
Any ideas ?
Thanks,
Eric
On Nov 16, 2010, at 7:46 AM, Gael Varoquaux wrote:
> Hey,
>
> Sorry for the slow reply,
>
> On Mon, Nov 15, 2010 at 11:52:41AM +0100, moscardi wrote:
>> # Code
>
>> import numpy as np
>
>> # Define the sphere cut in two
>
>> xdim, ydim, zdim = 50, 50, 50
>> vx, vy, vz = 1., 1., 1.
>> R = 25
>> cx = 25
>> cy = 25
>> cz = 25
>> data = np.zeros([xdim, ydim, zdim],np.uint8)
>> for i in xrange(xdim):
>> for j in xrange(ydim):
>> for k in xrange(zdim):
>> if (i * vx - cx)**2 + (j * vy - cy)**2 + (k * vz - cz)**2 < (R
>> * R) :
>> data[i,j,k] = 1
>> data[:,:,24:26] = 0
>
>> # Using of "Tvtk segmentation example" from mayavi
>> # to display the sphere
>
>> from enthought.mayavi import mlab
>> from enthought.tvtk.api import tvtk
>> fig = mlab.figure(bgcolor=(0, 0, 0), size=(400, 500))
>> fig.scene.disable_render = True
>> src = mlab.pipeline.scalar_field(data)
>> src.update_image_data = True
>> contour = mlab.pipeline.contour(src, )
>> #contour.filter.contours = [1,]
>> contour.filter.number_of_contours = 2
>> #connect_ = tvtk.PolyDataConnectivityFilter(extraction_mode=4)
>> connect_ = tvtk.PolyDataConnectivityFilter(extraction_mode=5)
>
> Here is your problem: you are using the 'all_regions' extraction mode
> of the connectivity filter (check in the pipeline GUI), so you are indeed
> getting all regions not differentiated.
>
> What you should do is select one regions, for instance using a
> 'closest_point', and create one actor for each region. I am attaching a
> modification of your script that does that.
>
> By the way: you have forgetten to set the disable_render flag back to
> False, so the updating was a bit awkward.
>
> HTH,
>
> Gael
> <tmp.py>
Eric MOSCARDI
INRIA - Virtual Plants
CIRAD, Avenue Agropolis
34398 Montpellier Cedex 5, France
04 67 61 58 00 (ask number 60 09)
email : [email protected]
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