| Re: Fill in a logic image: possible in IDL ? [message #24708] |
Mon, 16 April 2001 09:41 |
Ivan Zimine
Messages: 40
Registered: February 1999
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Member |
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jsilva@ci.uc.pt wrote:
>
> Hello
> To explain what I?m trying to do about a FILL in a logic image, I give an
> example (see the Computer Tomography lung image in
> http://www.ci.uc.pt/pessoal/jsilva/idl_fill.jpg )
> Thanks in advance for any suggestion.
> Jose Silva
> Physics Dep., FCTUC, Portugal
>
mask = byte(median(image gt 50, 9))
roi = search2d(mask, 0, 510, 0, 0)
msk1 = mask*0b
msk1[roi] = 1
roi = search2d(mask, 27, 32, 0, 0)
msk2 = mask*0b
msk2[roi] = 1
back_mask = msk1 or msk2
image_mask = 1 - back_mask
--
Ivan Zimine | ivan.zimine@physics.unige.ch
Dpt. of Radiology | (+41 22) 372 70 70
Geneva University Hospitals |
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| Re: Fill in a logic image: possible in IDL ? [message #24712 is a reply to message #24708] |
Sun, 15 April 2001 12:10  |
John-David T. Smith
Messages: 384
Registered: January 2000
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Senior Member |
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jsilva@ci.uc.pt wrote:
>
> Hello
> To explain what I?m trying to do about a FILL in a logic image, I give an
> example (see the Computer Tomography lung image in
> http://www.ci.uc.pt/pessoal/jsilva/idl_fill.jpg )
> Thanks in advance for any suggestion.
> Jose Silva
> Physics Dep., FCTUC, Portugal
OK, I think I see now... you want to do blob coloring, aka "fill" from
your favorite paint program. The IDL function label_region works well
for this. It's quite simple. The JHU library contains two example
programs for this, but I'll summarize:
labels=label_region(image LE level)
image[where(labels eq labels[x,y])]=fill
OK, so what does this do? label_region finds continuous blobs of
non-zero values, and gives them a non-zero "ID". You find the ID of
seed pixel (x,y), and where that blob exists in the array, then setting
this region to whatever fill value you like.
Note that all edge pixels are considered to be in no region
(label_region returns zero there). This seems dumb to me... one
workaround is to fill dummy rows and columns on the exterior with 1's.
You should probably also test that the region exists, or else you'll end
up filling all the pixels in no region. e.g.
if labels[x,y] ne 0 then ...
Another JHU program illustrates the flexibility of this method... since
you can make masks in many ways, you can label all sorts of interesting
things like boundary regions... the inverse of the former problem:
labels=label_region(image ne boundary)
or even
labels=label_region(image gt bmax OR image lt bmin)
Here we label all areas bordered by boundary values in some range.
Search2D can do this too, but I think label_region gives more
flexibility. Since it just finds regions of non-zero value in a mask,
you can conceive of doing all sorts of cool things. Here are a few
interesting challenges:
1. Region of strictly decreasing value from a seed pixel. Or try
increasing.
2. Region contiguous to seed pixel which is within 10% of the full data
range to it.
3. Region contiguous to seed pixel with values in the nearest Nth
percentile (think histogram).
4. Region contiguous to seed pixel which alternate even to odd.
etc.
Good luck,
JD
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| Re: Fill in a logic image: possible in IDL ? [message #24713 is a reply to message #24712] |
Sun, 15 April 2001 07:58 |
jsilva
Messages: 1
Registered: April 2001
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Junior Member |
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Hello
To explain what I�m trying to do about a FILL in a logic image, I give an
example (see the Computer Tomography lung image in
http://www.ci.uc.pt/pessoal/jsilva/idl_fill.jpg )
Thanks in advance for any suggestion.
Jose Silva
Physics Dep., FCTUC, Portugal
In article <3AD969AE.1A198238@physics.unige.ch>, Ivan Zimine says...
>
> Jose Silva wrote:
>>
>> Hello
>> I have a grayscale image (512 x 512 x 1 byte from medical TAC).
>> I applied a threshold to have a logic mask and tried to do a fill in that
>> mask
>> in order to remove some background. Most of languages have a fill command,
>> like FILL in draw programs that FILLs the image starting in X,Y (user
>> defined)
>> coordenations.
>> I search throw IDL commands and I never found any FILL command (or identical
>> command).
>> As most of languages (eg MATLAB and many others) have a FILL (BWFILL in
>> MATLAB, as morphologic operation), did I miss the FILL in IDL or there isn?t
>> any FILL in IDL?
>
> IDL> ?search2d
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| Re: Fill in a logic image: possible in IDL ? [message #24715 is a reply to message #24713] |
Sun, 15 April 2001 02:28 |
Ivan Zimine
Messages: 40
Registered: February 1999
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Member |
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Jose Silva wrote:
>
> Hello
> I have a grayscale image (512 x 512 x 1 byte from medical TAC).
> I applied a threshold to have a logic mask and tried to do a fill in that
> mask
> in order to remove some background. Most of languages have a fill command,
> like FILL in draw programs that FILLs the image starting in X,Y (user
> defined)
> coordenations.
> I search throw IDL commands and I never found any FILL command (or identical
> command).
> As most of languages (eg MATLAB and many others) have a FILL (BWFILL in
> MATLAB, as morphologic operation), did I miss the FILL in IDL or there isn?t
> any FILL in IDL?
IDL> ?search2d
--
Ivan Zimine | ivan.zimine@physics.unige.ch
Dpt. of Radiology | (+41 22) 372 70 70
Geneva University Hospitals |
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| Re: Fill in a logic image: possible in IDL ? [message #24716 is a reply to message #24715] |
Sat, 14 April 2001 19:27 |
John-David T. Smith
Messages: 384
Registered: January 2000
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Senior Member |
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jsilva@ci.uc.pt wrote:
>
> Hello
> I have a grayscale image (512 x 512 x 1 byte from medical TAC).
> I applied a threshold to have a logic mask and tried to do a fill in that mask
> in order to remove some background. Most of languages have a fill command, like
> FILL in draw programs that FILLs the image starting in X,Y (user defined)
> coordenations.
> I search throw IDL commands and I never found any FILL command (or identical
> command).
> As most of languages (eg MATLAB and many others) have a FILL (BWFILL in MATLAB,
> as morphologic operation), did I miss the FILL in IDL or there isn?t any FILL in
> IDL?
> I tried to use POLYFILL but my mask is very irregular, not being possible to
> apply a POLYFILL in a predefined region.
> Any commend on this subject is welcome?
>
> level=100
> mask= (image LE level) ; TAC of lungs (from TAC) with many irregularities
> ; FILL to ?fill? mask starting (eg) in 1,1 pixel coordination
>
> jsilva @ ci.uc.pt
Unless I've misunderstood, it's probably easier than you think:
mask=where(image LE level,cnt)
if cnt gt 0 then image[mask]=background
or, if you know for sure there are some elements in the mask, you can
just do:
image[where(image LE level)]=background
Notice that here mask is just a list of indices. You can use multiple
masks in one of two (or more) ways, e.g.:
1. immask=image LE level AND image GE otherlevel AND otherim eq 1
mask=where(immask ne 0)
2. mask=where(image LE level)
mask=mask[where(image[mask] GE otherlevel)]
mask=mask[where(otherim[mask] eq 1)]
In case 1, you compute all the comparisons on all the elements of image,
and AND them all together. In case 2, you examine only those elements
which survived the previous test, paring down mask at each step. Both
forms have their advantages. But getting used to lists of indices as
masks or collections of pixels in IDL is vital.
Good luck,
JD
P.S. Here's one other method which doesn't use subscripts, more in line
with your original idea:
mask=image LE level
image=image*(mask)+background*(mask eq 0)
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