| Image activities mapped to colorbar [message #11888] |
Thu, 04 June 1998 00:00 |
enkpong
Messages: 14
Registered: April 1997
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Junior Member |
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Hi folks,
I have some data sets of SPECT images that I want to display in a
window. For example:
IDL> for i=0,30 do tvscl, ImageSeq(*,*,i), i
where "ImageSeq" is a 3D FLTARR which contains a particular slice of the
brain. Since the images represent the activities in the brain at different
time, if I display the images with the above way, all of the images would
be scaled to their own maxima. What I want to do is to display the images
according to their activities and mapped the activities to a color bar so
that the first image frame may appear black while the last frame may
appear grey/white with background still black (assume that I use B/W for
display). How can I do that ??
Any hints would be greatly appreciated !!
KP.
--
Koon-pong Wong Email : enkpong@en.polyu.edu.hk
Department of Electronic Engineering
The Hong Kong Polytechnic University Phone : (+852) 2766 6201
Hung Hom, Kowloon FAX : (+852) 2362 8439
Hong Kong Office: DE503d
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| Re: Image activities mapped to colorbar [message #11890 is a reply to message #11888] |
Wed, 03 June 1998 00:00  |
davidf
Messages: 2866
Registered: September 1996
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Senior Member |
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Koon-Pong Wong (enkpong@encserver.en.polyu.edu.hk) writes:
> I have some data sets of SPECT images that I want to display in a
> window. For example:
>
> IDL> for i=0,30 do tvscl, ImageSeq(*,*,i), i
>
> where "ImageSeq" is a 3D FLTARR which contains a particular slice of the
> brain. Since the images represent the activities in the brain at different
> time, if I display the images with the above way, all of the images would
> be scaled to their own maxima. What I want to do is to display the images
> according to their activities and mapped the activities to a color bar so
> that the first image frame may appear black while the last frame may
> appear grey/white with background still black (assume that I use B/W for
> display). How can I do that ??
Here is the very first rule I teach in my IDL programming
classes:
If color is important to you never, NEVER use TVSCL!
It appears color is important to you here, so what you
have to do is scale the data using the BYTSCL command
and display it with the TV command.
Suppose, for example, that you want to scale the data
into the number of colors you have on your display.
(How many is that? You may not know. You certainly
can't be sure of it. That is *exactly* why you don't
want to be using TVSCL.) But suppose you can count on
200 colors on the monitors your data will typically be
display on.
And suppose that you want to scale the data linearly
between the data values of 10 and 1550. (Let's assume
your data is integer data.) Then you would display the
data like this:
IDL> scaledData = BytScl(ImageSeq, Top=199, Min=10, Max=1550)
IDL> FOR j=0,30 DO TV, scaledData(*,*,j), j
Now you will see *exactly* what you hoped to see!
These ideas are spelled out in excruciating detail in
my IDL Programming Techniques book. :-)
Cheers,
David
-----------------------------------------------------------
David Fanning, Ph.D.
Fanning Software Consulting
E-Mail: davidf@dfanning.com
Phone: 970-221-0438
Coyote's Guide to IDL Programming: http://www.dfanning.com/
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| Re: Image activities mapped to colorbar [message #11978 is a reply to message #11888] |
Thu, 04 June 1998 00:00 |
David Foster
Messages: 341
Registered: January 1996
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Senior Member |
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Koon-Pong Wong wrote:
>
> Hi folks,
>
> I have some data sets of SPECT images that I want to display in a
> window. For example:
>
> IDL> for i=0,30 do tvscl, ImageSeq(*,*,i), i
>
> where "ImageSeq" is a 3D FLTARR which contains a particular slice of the
> brain. Since the images represent the activities in the brain at different
> time, if I display the images with the above way, all of the images would
> be scaled to their own maxima. What I want to do is to display the images
> according to their activities and mapped the activities to a color bar so
> that the first image frame may appear black while the last frame may
> appear grey/white with background still black (assume that I use B/W for
> display). How can I do that ??
Koon-Pong -
You might be interested in a program I wrote called SHOW_IMG that
allows you to display a wide variety of medical images in a variety
of different window configurations. This program can read many different
medical image formats, so long as the images are square, with dimensions
of either {64, 128, 256 or 512}; the image data must be in raw 8-bit
or 16-bit format; there can be an initial header of unknown size, the
image reader will skip over it appropriately.
You say that your images are FLTARR. Is this after pre-processing?
As far as I understand it, SPECT images in raw form are usually
16-bit signed integer data.
You can get this program and many other routines related to medical
imaging at:
ftp://bial8.ucsd.edu pub/software/idl/share
You can download just the SHOW_IMG program and it's required routines,
or get a larger set of routines. There's a README file listing the
routines and their use. All are written for UNIX, most should work
on Windows/Mac without much work. All routines/programs have .doc
documentation files; you can use my LHELP program to view these
easily.
Hope this helps.
Dave
--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~
David S. Foster Univ. of California, San Diego
Programmer/Analyst Brain Image Analysis Laboratory
foster@bial1.ucsd.edu Department of Psychiatry
(619) 622-5892 8950 Via La Jolla Drive, Suite 2240
La Jolla, CA 92037
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~
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