| Re: XROI - how to invoke region growing [message #29223] |
Sat, 09 February 2002 12:19  |
Benno Puetz
Messages: 16
Registered: March 2000
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Junior Member |
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Ted Cary wrote:
> Oh. I have IDL 5.4 and no demo. I feel even more stupid. But maybe I
> could use a "region grow"... where can I read about it, since I don't have
> the demo or 5.5?
>
It is described in the whatsnew55.pdf file that is distributed with 5.5
which seems to be identical to the whatsnew.pdf that you can find on
RSI's site
http://www.rsinc.com/idl/whatsnew.cfm
It looks quite interesting - thanks for pointing it out
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| Re: XROI - how to invoke region growing [message #29224 is a reply to message #29223] |
Sat, 09 February 2002 05:49  |
Ted Cary
Messages: 53
Registered: October 2001
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Member |
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Oh. I have IDL 5.4 and no demo. I feel even more stupid. But maybe I
could use a "region grow"... where can I read about it, since I don't have
the demo or 5.5?
"David Fanning" <david@dfanning.com> wrote in message
news:MPG.16ce4dad81bcbe59897fe@news.frii.com...
> David Fanning (david@dfanning.com) writes:
>
>> I don't think XROI is what you want, although
>> I have used SEARCH2D to fairly good effect.
>> You could use your XROI selection to get
>> the values and seed point for the SEARCH2D
>> criteria.
>
> It has been brought to my attention that the XROI demo
> in the IDL demo distributed with IDL 5.5 does in fact
> have a button that allows one to set the "Region Grow"
> properties of the ROI. Apparently the demo takes
> advantage of a new function in IDL named (oddly enough)
> REGION_GROW. You can read all about this in the on-line
> he...er, well, you can read all about it somewhere (I'm
> sure).
>
> Apparently REGION_GROW does much of what SEARCH2D
> used to do, but adds the capability of doing it
> in 3D, something my ...uh, wife found interesting. :-)
>
> Cheers,
>
> David
>
> --
> David W. Fanning, Ph.D.
> Fanning Software Consulting
> Phone: 970-221-0438, E-mail: david@dfanning.com
> Coyote's Guide to IDL Programming: http://www.dfanning.com/
> Toll-Free IDL Book Orders: 1-888-461-0155
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| Re: XROI - how to invoke region growing [message #29226 is a reply to message #29224] |
Fri, 08 February 2002 20:04 |
David Fanning
Messages: 11724
Registered: August 2001
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Senior Member |
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David Fanning (david@dfanning.com) writes:
> I don't think XROI is what you want, although
> I have used SEARCH2D to fairly good effect.
> You could use your XROI selection to get
> the values and seed point for the SEARCH2D
> criteria.
It has been brought to my attention that the XROI demo
in the IDL demo distributed with IDL 5.5 does in fact
have a button that allows one to set the "Region Grow"
properties of the ROI. Apparently the demo takes
advantage of a new function in IDL named (oddly enough)
REGION_GROW. You can read all about this in the on-line
he...er, well, you can read all about it somewhere (I'm
sure).
Apparently REGION_GROW does much of what SEARCH2D
used to do, but adds the capability of doing it
in 3D, something my ...uh, wife found interesting. :-)
Cheers,
David
--
David W. Fanning, Ph.D.
Fanning Software Consulting
Phone: 970-221-0438, E-mail: david@dfanning.com
Coyote's Guide to IDL Programming: http://www.dfanning.com/
Toll-Free IDL Book Orders: 1-888-461-0155
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| Re: XROI - how to invoke region growing [message #29230 is a reply to message #29228] |
Fri, 08 February 2002 16:06 |
David Fanning
Messages: 11724
Registered: August 2001
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Senior Member |
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Dr. Stefan P. Mueller (stefan.mueller@uni-essen.de) writes:
> XROI looks like a good starting point for what I am planning to do:
> define a region-of-interest on a CT scan by region growing (to segment
> reproducible a lesion) and then go on to sovle my real problem.
> I just installed the demo for IDL 5.5 and ran XROI. I am able to
> display the CT Image. I can manually define all sorts of ROI's, and I
> can get statistics or a histogram. I have been unable, however, to
> figure out how to invoke the region growing function. Yes, I looked at
> the dokumentation too.
> As a beginner, trying to understand the code (probably over 50 pages)
> is daunting to me...
>
> Does anybody know what I have to do?
I don't think XROI is what you want, although
I have used SEARCH2D to fairly good effect.
You could use your XROI selection to get
the values and seed point for the SEARCH2D
criteria.
Cheers,
David
--
David W. Fanning, Ph.D.
Fanning Software Consulting
Phone: 970-221-0438, E-mail: david@dfanning.com
Coyote's Guide to IDL Programming: http://www.dfanning.com/
Toll-Free IDL Book Orders: 1-888-461-0155
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| Re: XROI - how to invoke region growing [message #29232 is a reply to message #29230] |
Fri, 08 February 2002 13:44 |
Ted Cary
Messages: 53
Registered: October 2001
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Member |
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Hello Dr. Mueller,
I'll have to ask you to excuse my ignorance as well, but to help with this
I need to know exactly what you mean by "region growing." I don't have
experience with XROI or CT scans, but I did not find any mention of the
region growing function you are trying to invoke during a quick reading of
the XROI help files. If something like this exists, I could use it too.
I'm not sure if region growing has a special meaning in your field, but
here are my suggestions, for what they're worth:
If you want to simply scale the regions, you can call scale methods on them
individually, since they are just IDLgrROI objects. It looks to me as
though you can get them using the REGIONS_OUT keyword to XROI, scale them
all, then use the scaled ROIs as the REGIONS_IN in another XROI call if you
want. Of course if the regions are concave, then the margins of your new
"grown" regions might actually intersect the margins of the smaller regions
from which they were grown, which might not be what you want at all, since
the grown region won't contain all of the points in the smaller region.
If instead you want to "expand" or dilate the regions, maybe POLYFILLV the
ROI vertices and use DILATE. The array results will not be in a form you
can put back into an IDLgrROI, since there will be no margin vertices
identified nor a connectivity array, but they will allow you to extract
data from your scans easily, and you can continue to DILATE or ERODE the
regions at will. Unfortunately, unless you "hull" the interior points to
get the connectivity array and the margin vertices, you won't be able to
use XROI on the regions you've grown. This method will work fine if all
you want to do is 1) Draw ROIs in XROI, 2) "Grow" or "shrink" them, and 3)
Extract data from their interiors. You can even display the new margins
if you want by finding the contours of the interiors--you'll know every
point on the border in no particular order, but not every vertex. I do
this kind of thing all the time, and it should not require any or much
modification to those 50 pages of XROI code. Hope this helps.
"Dr. Stefan P. Mueller" wrote:
> Hi,
>
> I am new to IDL, so please excuse my ignorance:
>
> XROI looks like a good starting point for what I am planning to do:
> define a region-of-interest on a CT scan by region growing (to segment
> reproducible a lesion) and then go on to sovle my real problem.
> I just installed the demo for IDL 5.5 and ran XROI. I am able to
> display the CT Image. I can manually define all sorts of ROI's, and I
> can get statistics or a histogram. I have been unable, however, to
> figure out how to invoke the region growing function. Yes, I looked at
> the dokumentation too.
> As a beginner, trying to understand the code (probably over 50 pages)
> is daunting to me...
>
> Does anybody know what I have to do?
>
> Thanks a lot!
>
> Stefan
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| Re: XROI - how to invoke region growing [message #29320 is a reply to message #29224] |
Sun, 10 February 2002 02:37 |
dw
Messages: 10
Registered: February 2001
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Junior Member |
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> David Fanning (david@dfanning.com) writes:
>> Apparently REGION_GROW does much of what SEARCH2D
>> used to do, but adds the capability of doing it
>> in 3D, something my ...uh, wife found interesting. :-)
>>
Do you know what the difference is then between the old SEARCH3D (5.4)
and the new REGION_GROW (in 5.5)? Also, are any of you familiar with a
3-d equivalent of CONTOUR? I use CONTOUR to retrieve perimeter, area
etc. for 2D objects (and thanks to this newsgroup and Dave Fanning I
have learnt that it's necessary to smooth the object before! using
CONTOUR to get decent results (error < 1%), but I don't think SURFACE
will do the same in 3D, i.e., give me surface area for instance, of a
3D object?
Cheers,
Dorthe
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| Re: XROI - how to invoke region growing [message #29356 is a reply to message #29320] |
Wed, 13 February 2002 06:05 |
David Fanning
Messages: 11724
Registered: August 2001
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Senior Member |
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Dorthe Wildenschild (dw@er.dtu.dk) writes:
> Do you know what the difference is then between the old SEARCH3D (5.4)
> and the new REGION_GROW (in 5.5)?
Haven't you had the experience of spending a week writing
a great new routine, only to accidentally discover that
you had written (and forgotten) something very much like
it the year before? I don't know that this is the case here,
but it seems like it. REGION_GROW is definitely more robust
than SEARCH3D (n-dimensional arrays vs. 3D arrays, for example),
but they do very similar things. I'd like to think of them as two
approaches to the same problem. You should try them both and see which
you like better.
> Also, are any of you familiar with a
> 3-d equivalent of CONTOUR? I use CONTOUR to retrieve perimeter, area
> etc. for 2D objects (and thanks to this newsgroup and Dave Fanning I
> have learnt that it's necessary to smooth the object before! using
> CONTOUR to get decent results (error < 1%), but I don't think SURFACE
> will do the same in 3D, i.e., give me surface area for instance, of a
> 3D object?
I should think either ISOCONTOUR or ISOSURFACE is what you
are looking for.
Cheers,
David
--
David W. Fanning, Ph.D.
Fanning Software Consulting
Phone: 970-221-0438, E-mail: david@dfanning.com
Coyote's Guide to IDL Programming: http://www.dfanning.com/
Toll-Free IDL Book Orders: 1-888-461-0155
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