| Calculate median of stacks of images using IDL [message #88707] |
Fri, 06 June 2014 13:46  |
oatty3931
Messages: 8
Registered: June 2014
|
Junior Member |
|
|
Hi,
I am trying to compute a median of a stack of images in TIF format for my research. From another source I found out a way to compute this from stack of images present in a GDF format, using
IDL> buf=read_gdf('demo.gdf')
IDL> help, buf
BUF FLOAT = Array[640, 480, 100]
IDL>b=median(buf,/double,dimension=3)
However, I am having difficulty converting my TIF images into GDF, but still need to normalize my images somehow. Any suggestions on how to do so?
Thank you in advance. Any help will be highly appreciated!
Nitsorn Wongsajjathiti
|
|
|
|
| Re: Calculate median of stacks of images using IDL [message #88708 is a reply to message #88707] |
Sat, 07 June 2014 15:42  |
dg86
Messages: 118
Registered: September 2012
|
Senior Member |
|
|
On Friday, June 6, 2014 4:46:37 PM UTC-4, Nitsorn Wongsajjathiti wrote:
> Hi,
>
> I am trying to compute a median of a stack of images in TIF format for my research. From another source I found out a way to compute this from stack of images present in a GDF format, using
>
>
>
> IDL> buf=read_gdf('demo.gdf')
>
> IDL> help, buf
>
> BUF FLOAT = Array[640, 480, 100]
>
> IDL>b=median(buf,/double,dimension=3)
>
>
>
> However, I am having difficulty converting my TIF images into GDF, but still need to normalize my images somehow. Any suggestions on how to do so?
>
> Thank you in advance. Any help will be highly appreciated!
>
> Nitsorn Wongsajjathiti
Hi Again,
You can use READ_IMAGE to read in your images, then stack them up, and take the median.
filenames = file_search("my_filename_regex*.tif")
buf = []
for f in filenames do $
buf = [[[buf]], [[read_image(f)]]]
b = median(buf, /double, dimension=3)
TTFN,
David
|
|
|
|
| Re: Calculate median of stacks of images using IDL [message #88709 is a reply to message #88707] |
Sun, 08 June 2014 12:06 |
Phillip Bitzer
Messages: 223
Registered: June 2006
|
Senior Member |
|
|
On Friday, June 6, 2014 3:46:37 PM UTC-5, Nitsorn Wongsajjathiti wrote:
> Hi,
>
> I am trying to compute a median of a stack of images in TIF format for my research. From another source I found out a way to compute this from stack of images present in a GDF format, using
>
>
>
> IDL> buf=read_gdf('demo.gdf')
>
So, I suppose READ_GDF is from another library, yes? Do you _need_ things in GDF?
If you have TIFFs, you can just use READ_TIFF, and create a 3d array like David suggests.
Depending on how many TIFFs you have, you may find this modification to David's snippet to be slightly more efficient:
filenames = file_search("my_filename_regex*.tif", COUNT=fileCount) ;get the filenames, and how many
isGood = QUERY_TIFF(filenames[0], tiffInfo) ;get information about the first TIFF file
;assuming the TIFFs are 8 bit....if 16bit you can change to UINTARR
buf = BYTARR([tiffInfo.resolution, fileCount]) ;assuming all TIFFs are the same size, preallocate the array
FOREACH f in filenames DO $
buf[0, 0, i] = READ_TIFF(f) ;read each TIFF into the buf array
b = median(buf, /double, dimension=3)
|
|
|
|
| Re: Calculate median of stacks of images using IDL [message #88710 is a reply to message #88708] |
Mon, 09 June 2014 04:18 |
dg86
Messages: 118
Registered: September 2012
|
Senior Member |
|
|
On Saturday, June 7, 2014 6:42:04 PM UTC-4, David Grier wrote:
> On Friday, June 6, 2014 4:46:37 PM UTC-4, Nitsorn Wongsajjathiti wrote:
>
>> Hi,
>
>>
>
>> I am trying to compute a median of a stack of images in TIF format for my research. From another source I found out a way to compute this from stack of images present in a GDF format, using
>
>>
>
>>
>
>>
>
>> IDL> buf=read_gdf('demo.gdf')
>
>>
>
>> IDL> help, buf
>
>>
>
>> BUF FLOAT = Array[640, 480, 100]
>
>>
>
>> IDL>b=median(buf,/double,dimension=3)
>
>>
>
>>
>
>>
>
>> However, I am having difficulty converting my TIF images into GDF, but still need to normalize my images somehow. Any suggestions on how to do so?
>
>>
>
>> Thank you in advance. Any help will be highly appreciated!
>
>>
>
>> Nitsorn Wongsajjathiti
>
>
>
> Hi Again,
>
>
>
> You can use READ_IMAGE to read in your images, then stack them up, and take the median.
>
>
>
> filenames = file_search("my_filename_regex*.tif")
>
> buf = []
>
> for f in filenames do $
>
> buf = [[[buf]], [[read_image(f)]]]
>
>
>
> b = median(buf, /double, dimension=3)
>
>
>
> TTFN,
>
>
>
> David
I was trying to avoid having to figure out the dimensions of the images. Here's a more general version:
buf = list()
for f in file_search("mynames*.tif") do $
buf.add, read_image(f)
b = median(buf.toarray(), /double, dimension=1)
This works for grayscale and color images, regardless of the pixel ordering.
TTFN,
David
|
|
|
|
|
|
|
|
|
|
|
|
| Re: Calculate median of stacks of images using IDL [message #88727 is a reply to message #88726] |
Tue, 10 June 2014 09:36 |
Michael Galloy
Messages: 1114
Registered: April 2006
|
Senior Member |
|
|
On 6/10/14, 10:18 AM, oatty3931@gmail.com wrote:
> Hi Mike,
> Thank you for your reply. Unfortunately, I still received an error after:
>
> IDL> buf=list()
> IDL> for f, file_search("mynames*.tif") do $
>> buf.add,read_image(f)
>
> for f, file_search("mynames*.tif") do $
> ^
> % Syntax error.
>
> I am using IDL 8.2.3, if that helps
> Thank you once again,
> Nitsorn
>
Sorry, still too much Python:
foreach f, file_search('mynames*.tif') do $
Mike
--
Michael Galloy
www.michaelgalloy.com
Modern IDL: A Guide to IDL Programming (http://modernidl.idldev.com)
Research Mathematician
Tech-X Corporation
|
|
|
|
|
|
| Re: Calculate median of stacks of images using IDL [message #88742 is a reply to message #88728] |
Wed, 11 June 2014 11:21 |
dg86
Messages: 118
Registered: September 2012
|
Senior Member |
|
|
On Tuesday, June 10, 2014 12:51:38 PM UTC-4, oatt...@gmail.com wrote:
> Thank you! That works perfectly :)
Egads! As Mike points out, I've been doing too much python programming recently.
I'm very sorry for the crumpled code example!
Sigh,
David
|
|
|
|
comp.lang.idl-pvwave archive
Members
Search
Help
Login
Home
