Posted by
Stephan Preibisch on
Nov 22, 2010; 8:33am
URL: http://imagej.273.s1.nabble.com/FIJI-2D-stitching-in-a-macro-solution-tp3686366p3686370.html
Hi,
I am happy this works out, and also that the major problem were the updated
field names...I will try to import the zig-zag macro into the stitching
plugin collection, thanks a lot Christophe!
Nice greetings,
Stephan
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Jacqui
Ross
Sent: Monday, November 22, 2010 5:53 AM
To:
[hidden email]
Subject: FIJI 2D stitching in a macro - solution!
Hi Everyone,
Christophe Leterrier has very kindly written a macro for me, which
solved my problem. This macro tiles the 3 images together perfectly
(even though they are a zigzag) and saves each tiled image as a separate
TIFF file. I was then able to open the sequence of tiled images as a
virtual stack and save out as AVI.
I have forwarded (below) the email that Christophe sent me as
explanation of the macro. I have also included one where I have
described the data that I sent him, so that you will know how the
folders work. It has taught me some useful information about how to
write these kinds of macros.
The macro is called Stitch BMT. I have copied it below. I hope the
formatting is preserved since it wasn't last time. The macro file itself
was rejected by the listserver.
macro "Stitch BMT" {
PARENT_PATH=getDirectory("Select a directory");
File.makeDirectory(PARENT_PATH+"tiled");
POSITION=newArray("bottom", "middle", "top");
ALL_NAMES=getFileList(PARENT_PATH+POSITION[0]+File.separator);
for (i=1; i<=ALL_NAMES.length; i++) {
BOTTOM_IMAGE=POSITION[0]+pad(i,3,0)+".tif";
MIDDLE_IMAGE=POSITION[1]+pad(i,3,0)+".tif";
TOP_IMAGE=POSITION[2]+pad(i,3,0)+".tif";
FUSED_IMAGE="fused"+pad(i,3,0)+".tif";
BOTTOM_PATH=PARENT_PATH+POSITION[0]+File.separator+BOTTOM_IMAGE;
MIDDLE_PATH=PARENT_PATH+POSITION[1]+File.separator+MIDDLE_IMAGE;
TOP_PATH=PARENT_PATH+POSITION[2]+File.separator+TOP_IMAGE;
FUSED_PATH=PARENT_PATH+File.separator+"tiled"+File.separator+FUSED_IMAGE
;
print("\n");
print("bottom: "+BOTTOM_IMAGE);
print("middle: "+MIDDLE_IMAGE);
print("top: "+TOP_IMAGE);
print("fused: "+FUSED_IMAGE);
open(BOTTOM_PATH);
open(MIDDLE_PATH);
open(TOP_PATH);
run("2D Stitching", "first_image="+
BOTTOM_IMAGE +" use_channel_for_first=[Red, Green and Blue]
second_image="+ MIDDLE_IMAGE +" use_channel_for_second=[Red, Green and
Blue] use_windowing how_many_peaks=5 create_merged_image
fusion_method=[Linear Blending] fusion=1.50 fused_image=temp.tif
compute_overlap x=0 y=0");
run("2D Stitching",
"first_image=temp.tif use_channel_for_first=[Red, Green and Blue]
second_image="+ TOP_IMAGE +" use_channel_for_second=[Red, Green and
Blue] use_windowing how_many_peaks=5 create_merged_image
fusion_method=[Linear Blending] fusion=1.50 fused_image="+ FUSED_IMAGE
+" compute_overlap x=0 y=0");
selectWindow(BOTTOM_IMAGE);
close();
selectWindow(MIDDLE_IMAGE);
close();
selectWindow(TOP_IMAGE);
close();
selectWindow("temp.tif");
close();
selectWindow(FUSED_IMAGE);
save(FUSED_PATH);
close();
}
}
function pad(number, width, character) {
number = toString(number); // force string
character = toString(character);
for (len = lengthOf(number); len < width; len++)
number = character + number;
return number;
}
I hope it will also be of use to others.
Thanks Christophe for your efforts!
Kind regards,
Jacqui
Jacqueline Ross
Biomedical Imaging Microscopist
Biomedical Imaging Research Unit
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, NEW ZEALAND
Tel: 64 9 373 7599 Ext 87438
Fax: 64 9 373 7484
http://www.fmhs.auckland.ac.nz/sms/biru/From: Christophe Leterrier [mailto:
[hidden email]]
Sent: Wednesday, 17 November 2010 10:27 p.m.
To: Jacqui Ross
Subject: Re: FIJI 2D stitching in a macro
Hi Jaqui,
The attached macro (Stitch_BTM.ijm) should run fine with the latest
Stitching plugin from Fiji (the one with the updated fields).
It runs OK on my setup for the attached folder (the same you sent me but
I removed the "Tiled" folder). Just run the macro, choose the
"Christophe" folder in the dialog (you have to choose the parent folder
that contains the "bottom", "middle" and "top" folders), it will create
an additional "tiled" folder where it will store the resulting images
with "fused00X.tif" names.
One caution : the folders inside the parent folder must be named exaclty
"bottom", "middle" and "top", these folders must only contain images
that are used for stitiching and no other files or images, and the
images must be named "bottom00X.tif", "middle00X.tif", "top00X.tif"
(with three digits).
Hope this helps,
Christophe
On Wed, Nov 17, 2010 at 06:31, Jacqui Ross <
[hidden email]>
wrote:
Hi Christophe,
Thanks very much for your kind offer to assist me.
As you suggested, I have attached a .zip file containing 4 folders, 3
of which contain the raw data to be tiled. The other folder (Tiled)
contains one merged image, which will give you an idea of the overlap,
which is around 30%. As you will see, it's not ideal because it doesn't
comprise a square/rectangle, which would be better.
However, the 2D Stitch plugin seemed to do this tiling effortlessly with
a nice result as you will see.
I will look forward to hearing how you get on with this. It's not super
urgent so whenever you have time to take a look will be fine.
Thanks!
Kind regards,
Jacqui
Jacqueline Ross
Biomedical Imaging Microscopist
Biomedical Imaging Research Unit
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, NEW ZEALAND
Tel: 64 9 373 7599 Ext 87438
Fax: 64 9 373 7484
http://www.fmhs.auckland.ac.nz/sms/biru/