Cyclic translation transform

[jerry novakk]

Hi!

I am using transform function in imageJ 1.43U. As it turns out the translation in a chosen direction
cuts out that part of the image which leaves the view window and fills the other side with white.
This means that I lose information that i still need.
I am trying to work out how to keep the sample symmetry like on the picture below:



Does anyone know if this can be fixed or if any adequate plugin exists?

Thank you,
Jerry

[Michael Schmid]

Hi Jerry,

for translation with periodic boundary conditions, I am not aware of any ImageJ built-in function or external plugin (it would be easy to write one).

What you could do is replicating the image, and then crop it at the desired position. I have a macro that replicates a single image (not a stack) by creating a stack of identical slices, then making a montage of the slices. I'll paste the code at the very bottom.
Mind possible line breaks introduced by the mailer; the line starting with
  run("Make Montage...
should end with
  font=12");

Michael
________________________________________________________________
On Jul 9, 2015, at 13:50, jerry novakk wrote:

> Hi!
>
> I am using transform function in imageJ 1.43U. As it turns out the
> translation in a chosen direction
> cuts out that part of the image which leaves the view window and fills the
> other side with white.
> This means that I lose information that i still need.
> I am trying to work out how to keep the sample symmetry like on the picture
> below:
>
> Jerry <http://imagej.1557.x6.nabble.com/file/n5013479/TRANS.png>
>
> Does anyone know if this can be fixed or if any adequate plugin exists?
>
> Thank you,
> Jerry

________________________________________________________________

macro 'Replicate 3x3 [F2]' {
  // Replicate an image periodically in x and y
  // Michael Schmid, Version May 2015

  xRepetitions=3;
  yRepetitions=3;

  nTotal = xRepetitions*yRepetitions;
  title = getTitle();
  run("Duplicate...", "title=tmp");
  dupID = getImageID();
  run("Select All");
  run("Copy");
  for (i=0; i<nTotal; i++) {
    run("Add Slice");
    run("Paste");
  }

  run("Make Montage...", "columns=&xRepetitions rows=&yRepetitions scale=1 first=1 last=&nTotal increment=1 border=0 font=12");
  rename(title+"_"+ xRepetitions+"x"+ yRepetitions);
  selectImage(dupID);
  close();

}

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[Krs5]

Dear Jerry,

Maybe the code below does what you want. Open your image and make an ROI of the area you want to translate.

waitForUser ("make selection");
getSelectionBounds(x, y, width, height);
run("Copy");
run("Select None");
run("Translate...", "x="+width+" y=0 interpolation=None");
makeRectangle(0, 0, width, height);
run("Paste");

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif



-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of jerry novakk
Sent: 09 July 2015 12:51
To: [hidden email]
Subject: Cyclic translation transform

Hi!

I am using transform function in imageJ 1.43U. As it turns out the translation in a chosen direction cuts out that part of the image which leaves the view window and fills the other side with white.
This means that I lose information that i still need.
I am trying to work out how to keep the sample symmetry like on the picture
below:

Jerry <http://imagej.1557.x6.nabble.com/file/n5013479/TRANS.png>

Does anyone know if this can be fixed or if any adequate plugin exists?

Thank you,
Jerry



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View this message in context: http://imagej.1557.x6.nabble.com/Cyclic-translation-transform-tp5013479.html
Sent from the ImageJ mailing list archive at Nabble.com.

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[jerry novakk]

Thank you both very much for your help! I'll try it out and see if it works.

[jerry novakk]

Here are three versions of macros for translations, wich I made from your propositions. The code is a little bit trashy and definitely not optimized, but it works fine for me. I had problems with translations with negative input so I had to combine makeRectangle.. and Specify.. to paste back out of bound parts of an image.

I thank you both again for your help and hope someone else finds this usefull.

--------------------------------------------------------------------------------------
//Periodic_Translation_TopLeft.txt

  getDimensions(W, H, dummy, dummy, dummy);

//Open your image and make an ROI of the area you want to translate to top left corner.

  waitForUser ("select area");
  getSelectionBounds(X, Y, dummy, dummy);

  Xc=W-X;
  Xm=-X;
  Yc=H-Y;
  Ym=-Y;

//translate horizontal

  run("Select All");
  run("Specify...", "Width=X Height=H x=0 y=0");
  run("Copy");
  run("Select None");
  run("Translate...", "x=Xm y=0 interpolation=None");
  run("Specify...", "Width=X Height=H x=Xc y=0");
  run("Paste");

//translate vertical

  run("Select All");
  run("Specify...", "Width=W Height=Y x=0 y=0");
  run("Copy");
  run("Select None");
  run("Translate...", "x=0 y=Ym interpolation=None");
  run("Specify...", "Width=W Height=H x=0 y=Yc");
  run("Paste");
  run("Select None");
-----------------------------------------------------------------------------------------

-----------------------------------------------------------------------------------------
//Periodic_Translation_Center.txt

  getDimensions(W, H, dummy, dummy, dummy);

//Open your image and make an ROI of the area you want to center translate.

  waitForUser ("select area to center");
  getSelectionBounds(X, Y, width, height);

  a=round((W-width)*0.5);
  b=round((H-height)*0.5);

//translate horizontal
 
  if (a<=X){
    dx=X-a;
    Xcopy= W-dx;
    run("Select All");
    run("Specify...", "Width="+dx+" Height="+H+" x=0 y=0");
    run("Copy");
    run("Select None");
    run("Translate...", "x=-"+dx+" y=0 interpolation=None");
//    makeRectangle(Xcopy, 0, dx, H);
    run("Specify...", "Width=dx Height=H x=Xcopy y=0");
    run("Paste");
  } else {
    dx=a-X;
    Xcopy= W-dx;
    run("Select All");
    run("Specify...", "Width="+dx+" Height="+H+" x="+Xcopy+" y=0");
    run("Copy");
    run("Select None");
    run("Translate...", "x="+dx+" y=0 interpolation=None");
    makeRectangle(0, 0, dx, H);
    run("Paste");
  }

//translate vertical

  if (b<=Y) {
    dy=Y-b;
    ycopy= H-dy;
    run("Select All");
    run("Specify...", "Width="+W+" Height="+dy+" x=0 y=0");
    run("Copy");
    run("Select None");
    run("Translate...", "x=0 y=-"+dy+" interpolation=None");
    run("Specify...", "Width=W Height=dy x=0 y=ycopy");
    run("Paste");
  } else {
    dy=b-Y;
    ycopy= H-dy;
    run("Select All");
    run("Specify...", "Width="+W+" Height="+dy+" x=0 y="+ycopy+"");
    run("Copy");
    run("Select None");
    run("Translate...", "x=0 y="+dy+" interpolation=None");
    makeRectangle(0, 0, W, dy);
    run("Paste");
  }

    run("Select None");

-----------------------------------------------------------------------------------------

-----------------------------------------------------------------------------------------
//Periodic_Translation_Input.txt

  getDimensions(W, H, dummy, dummy, dummy);

//translate horizontal

  Dialog.create("Translate horizontal");
  Dialog.addNumber("X", 0);
  Dialog.show();
  X= Dialog.getNumber();
 
  if (X<0) {
    Xa=W+X;
    run("Select All");
    run("Specify...", "Width=abs(X) Height=H x=0 y=0");
    run("Copy");
    run("Select None");
    run("Translate...", "x=X y=0 interpolation=None");
    run("Specify...", "Width=abs(X) Height=H x=Xa y=0");
    run("Paste");
  }
  else {
    Xb=W-X;
    run("Select All");
    run("Specify...", "Width=abs(X) Height=H x=Xb y=0");
    run("Copy");
    run("Select None");
    run("Translate...", "x=X y=0 interpolation=None");
    makeRectangle(0, 0, abs(X), H);
    run("Paste");
  }


//translate vertical

  Dialog.create("Translate vertical");
  Dialog.addNumber("Y", 0);
  Dialog.show();
  Y= Dialog.getNumber();

  if (Y<0) {
    Ya=H+Y;
    run("Select All");
    run("Specify...", "Width=W Height=abs(Y) x=0 y=0");
    run("Copy");
    run("Select None");
    run("Translate...", "x=0 y=Y interpolation=None");
    run("Specify...", "Width=W Height=abs(Y) x=0 y=Ya");
    run("Paste");
  }
  else {
    Yb=H-Y;
    run("Select All");
    run("Specify...", "Width=W Height=abs(Y) x=0 y=Yb");
    run("Copy");
    run("Select None");
    run("Translate...", "x=0 y=Y interpolation=None");
    makeRectangle(0, 0, W, abs(Y));
    run("Paste");
  }
 
  run("Select None");
----------------------------------------------------------------------------------

[jerry novakk]

Below I've added a Macro that periodically Translates all images in a stack for the same input amount in x & y direction.

__________________________________________________________________________________________

//Stack needs to be open!!

Dialog.create("Translate horizontal");
Dialog.addNumber("X", 0);
Dialog.show();
X= Dialog.getNumber();

Dialog.create("Translate vertical");
Dialog.addNumber("Y", 0);
Dialog.show();
Y= Dialog.getNumber();

for(i=1;i<=nSlices;i++){
  setSlice(i);

    getDimensions(W, H, dummy, dummy, dummy);

  //translate horizontal

    if (X<0) {
      Xa=W+X;
      run("Select All");
      run("Specify...", "Width=abs(X) Height=H x=0 y=0");
      run("Copy");
      run("Select None");
      run("Translate...", "x=X y=0 interpolation=None");
      run("Specify...", "Width=abs(X) Height=H x=Xa y=0");
      run("Paste");
    }
    else {
      Xb=W-X;
      run("Select All");
      run("Specify...", "Width=abs(X) Height=H x=Xb y=0");
      run("Copy");
      run("Select None");
      run("Translate...", "x=X y=0 interpolation=None");
      makeRectangle(0, 0, abs(X), H);
      run("Paste");
    }

  //translate vertical
 
    if (Y<0) {
      Ya=H+Y;
      run("Select All");
      run("Specify...", "Width=W Height=abs(Y) x=0 y=0");
      run("Copy");
      run("Select None");
      run("Translate...", "x=0 y=Y interpolation=None");
      run("Specify...", "Width=W Height=abs(Y) x=0 y=Ya");
      run("Paste");
    }
    else {
      Yb=H-Y;
      run("Select All");
      run("Specify...", "Width=W Height=abs(Y) x=0 y=Yb");
      run("Copy");
      run("Select None");
      run("Translate...", "x=0 y=Y interpolation=None");
      makeRectangle(0, 0, W, abs(Y));
      run("Paste");
    }
 
    run("Select None");
}

__________________________________________________________________________________________