correcting a constant drift in a image stack

[Wes Armour]

Hi all,

I have a series of images (600) that have a constant drift of 1/30 of a
pixel between frames. I have tried various align plugins but none seem to work.
This doesn't surprise me because the main object in the images changes.

Is there a way I can do an incremental translation to the images?
For example...
Translate image1 by 1x0.0333 in x
Translate image2 by 2x0.0333 in x
Translate image3 by 3x0.0333 in x
Translate image4 by 4x0.0333 in x

Thanks for any help,

Wes.

[jiho]

On 2009-March-17  , at 11:34 , Wes wrote:

> Translate image1 by 1x0.0333 in x
> Translate image2 by 2x0.0333 in x
> Translate image3 by 3x0.0333 in x
> Translate image4 by 4x0.0333 in x

I am not sure this would apply to subpixel movement but you could  
batch shift the source images by the amount of drift using  
ImageMagick. Here is a small shell script template:

#!/bin/sh
# Assuming images are named like IMG001.JPG, IMG002.JPG, etc. and the  
shift is from left to right
# To adapt to your own scenario

# Get width and height of the first image
width=`identify -format "%[fx:w]" IMG001.JPG`
height=`identify -format "%[fx:h]" IMG001.JPG`
echo $width
echo $height

# Create temporary dir to work in
mkdir tmp

nbImages=3
for (( i = 1; i <= $nbImages; i++ )); do
     # Compute the amount of pixels to translate the image by
     moveBy=`echo $i*0.0333` | bc

     # Construct the name of the current image
     curImg="IMG"$(printf "%03i" $i)".JPG"

     # Recrop image, translating the frame to the right by $moveBy  
pixels
     # At the right of the image, the image is "wrapped" around the  
"missing" pixels are filled with the pixels from the left
     convert -crop "$width"x"$height"+"$moveBy"+0! $curImg tmp/"$curImg"
done

# At this point the images in tmp/ have all the same size and are  
shifted to a common reference.

exit 0


I hope that helps.

Jean-Olivier Irisson
---
Division of Applied Marine Physics
Rosenstiel School of Marine and Atmospheric Sciences
4600 Rickenbacker Causeway, Miami, Florida 33149-1098
[phone]
http://jo.irisson.free.fr/work/

[Wayne Rasband]

On Mar 17, 2009, at 11:34 AM, Wes wrote:

> Hi all,
>
> I have a series of images (600) that have a constant drift of 1/30 of a
> pixel between frames. I have tried various align plugins but none seem
> to work.
> This doesn't surprise me because the main object in the images changes.
>
> Is there a way I can do an incremental translation to the images?
> For example...
> Translate image1 by 1x0.0333 in x
> Translate image2 by 2x0.0333 in x
> Translate image3 by 3x0.0333 in x
> Translate image4 by 4x0.0333 in x

Here is a macro that will correct for the drift:

   requires("1.42l");
   setBatchMode(true);
   drift = 0.0333;
   offset = 0;
   for (i=1; i<=nSlices; i++) {
      setSlice(i);
      offset += drift;
      run("Translate...", "interpolation=Bicubic slice y=0 x="+offset);
   }

It requires the v1.42l daily build, which updates the Image>Translate
command to work with sub-pixel offsets. V1.42l also adds a Bicubic
interpolation option to the Translate, Scale, Rotate and Adjust>Size
commands. The bicubic interpolation method used is from Chapter 16 of
"Digital Image Processing: An Algorithmic Introduction Using Java" by
Wilhelm Burger and Mark Burge. The 'a' control parameter is set to 0.5
(Catmull-Rom interpolation). You can update to the daily build by using
the Help>Update ImageJ command and selecting "daily build" from the
drop down menu.

-wayne

[Wes Armour]

Many thanks for your replies Wayne and Jean-Olivier,

I did try the convert script but it only gives pixel level alignment.
The macro worked far better giving sub-pixel alignment which is what I
needed.

Cheers,

Wes.

On Tue, 2009-03-17 at 16:14 -0400, Wayne Rasband wrote:

> On Mar 17, 2009, at 11:34 AM, Wes wrote:
>
> > Hi all,
> >
> > I have a series of images (600) that have a constant drift of 1/30 of a
> > pixel between frames. I have tried various align plugins but none seem
> > to work.
> > This doesn't surprise me because the main object in the images changes.
> >
> > Is there a way I can do an incremental translation to the images?
> > For example...
> > Translate image1 by 1x0.0333 in x
> > Translate image2 by 2x0.0333 in x
> > Translate image3 by 3x0.0333 in x
> > Translate image4 by 4x0.0333 in x
>
> Here is a macro that will correct for the drift:
>
>    requires("1.42l");
>    setBatchMode(true);
>    drift = 0.0333;
>    offset = 0;
>    for (i=1; i<=nSlices; i++) {
>       setSlice(i);
>       offset += drift;
>       run("Translate...", "interpolation=Bicubic slice y=0 x="+offset);
>    }
>
> It requires the v1.42l daily build, which updates the Image>Translate
> command to work with sub-pixel offsets. V1.42l also adds a Bicubic
> interpolation option to the Translate, Scale, Rotate and Adjust>Size
> commands. The bicubic interpolation method used is from Chapter 16 of
> "Digital Image Processing: An Algorithmic Introduction Using Java" by
> Wilhelm Burger and Mark Burge. The 'a' control parameter is set to 0.5
> (Catmull-Rom interpolation). You can update to the daily build by using
> the Help>Update ImageJ command and selecting "daily build" from the
> drop down menu.
>
> -wayne

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