Greetings Jeremy,
does that mean that something is wrong with my macro?
At least your macro doesn't work for me with the "riceSeeds" test image
while both of my macros do.
Thanks anyway
Herbie
:::::::::::::::::::::::::::::::::::::::::
Am 24.01.25 um 11:00 schrieb Jeremy Adler:
This macro happily rotates the individual selections and makes them into a
montage.
Note I reduced the image to 8 bit to simplify thresholding, but the method
works on RGB images
run("8-bit");
setAutoThreshold("Huang dark no-reset");
run("Create Selection");
run("Fill", "slice");
run("Select None");
setThreshold(0,254);
UseImageID=getImageID();
roiManager("reset");
run("Analyze Particles...", "size=200-Infinity add");
//resetThreshold;
Nrois=roiManager("count");
for (i = 0; i <= Nrois-1; i++) {
selectImage(UseImageID);
roiManager("select", i);
run("Fit Rectangle");
run("Duplicate...", " ");
rename("blob"+i);
}
run("Images to Stack", " title=blob fill=#ffffff use keep");
run("Make Montage...", "columns=1 rows=Nrois scale=1 border=4 use");
Jeremy
===============================================
B i o V i s P l a t f o r m of Uppsala University
Light & EM microscopy / FlowCytometry & Cell Sorting /
Image Analysis
===============================================
Jeremy Adler PhD - Senior research engineer
Light, Confocal Microscopy, Image Analysis
E-mail: [email protected]
0739 188170
www.uu.se/biovis
Dag Hammarskjölds v 20
751 85 UPPSALA, SWEDEN
http://biovis.uu.se/
===============================================
-----Original Message-----
From: Herbie <[email protected]>
Sent: Thursday, January 23, 2025 4:19 PM
To: [email protected]
Subject: Re: can't rotate pasted image
Thanks Kees,
this was of course a typo in my mail.
It doesn't change the problem!
Thanks
Herbie
:::::::::::::::::::::::::::::::::::::::::::::::::::
Am 23.01.25 um 14:56 schrieb Straatman, Kees (Dr.):
Hi Herbie,
It should be:
run("Images to Stack","name=Seeds title=#");
setBatchMode(false);
exit();
Best wishes
Kees
Advanced Imaging Facility (RRID: SCR_020967) University of Leicester
http://www.le.ac.uk/advanced-imaging-facility
-----Original Message-----
Sent: 23 January 2025 12:56
Subject: Re: can't rotate pasted image
***CAUTION:*** This email was sent from an EXTERNAL source. Think before
clicking links or opening attachments.
Dear Jeremy,
dear listers!
Attached please find my macro with the mechanism suggested by Jeremy!
Interestingly, I wasn't able to make it work properly with
run("Images to Stack","name=Seeds title=#");
setBatchMode(true);
exit();
instead of
setBatchMode("exit and display");
run("Images to Stack","name=Seeds title=#");
exit();
In the former case, all slices are magically doubled.
Regards
Herbie
:::::::::::::::::::::::::::::::::::::::::
Am 22.01.25 um 18:32 schrieb Jeremy Adler:
A slightly simpler variant on Herbie's macro.
Once you have a selection for single objects, use "Fit Rectangle" and then
duplicate.
The duplicated part of the image is rotated.
Jeremy
===============================================
B i o V i s P l a t f o r m of Uppsala University
Light & EM microscopy / FlowCytometry & Cell
Sorting / Image Analysis ===============================================
Jeremy Adler PhD - Senior research engineer
Light, Confocal Microscopy, Image Analysis
E-mail: [email protected]
0739 188170
http://www.u/
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===============================================
-----Original Message-----
From: Herbie <[email protected]>
Sent: Wednesday, January 22, 2025 3:57 PM
To: [email protected]
Subject: Re: can't rotate pasted image
Slightly off-topic William!
Some years ago I was asked to write a macro that performs this task on rice
seeds.
Attached please find the "revived" macro-code and a test-image.
The macro requires two ImageJ-plugins.
Good to hear you resolved the Java-problem.
Regards
Herbie
:::::::::::::::::::::::::::::::::::::::::
Am 22.01.25 um 13:04 schrieb William Rust:
I'm writing code in java. What I am trying to do is take an image
with
20 wheat kernels in a petri dish and put each kernel in its own
image with the kernel rotated so all kernels are roughly vertical.
Here's the code snippet where I am doing it.
ImageProcessor newIp = new ColorProcessor(300, 300);
ImagePlus newImp = new ImagePlus("sub " + idx, newIp);
newIp.setColor(background);
newIp.fill();
imp.copy();
newImp.paste();
newImp.getProcessor().rotate(angle[idx]);
newImp.updateAndDraw();
newImp.show();
Previously, I've cut the subimage out of the original image using
the bounding box from analyze particles. The weirdness occurs
somewhere between the paste and the rotate. The pasting works whether I do the
rotate or not.
But when I paste, the rotate does not work. And, if I don't paste,
the rotate does work (I can tell this because the background is
tilted after a rotate with no paste but not with rotate and paste).
This snippet shows one of the things that I've tried, the updateAndDraw(), but
nothing has worked.
Any ideas on what I'm doing wrong?
Thanks,
wjr.
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//imagej-macro "seeds2stack" (Herbie G., 22. Jan. 2025)
/*
Requires two ImageJ-plugins "RGB_to_CMYK.class"
<https://imagej.net/ij/plugins/cmyk/index.html>
and "Angular_Deviation.class"
<https://www.gluender.de/Miscellanea/MiscTexts/UtilitiesText.html#Gl-2018-3>
*/
requires("1.54m");
setForegroundColor(255,255,255);
setBackgroundColor(0,0,0);
run("Remove Overlay");
ttl=getTitle();
setBatchMode(true);
run("RGB to CMYK");
setSlice(2);
setAutoThreshold("Intermodes dark no-reset");
run("Analyze Particles...","add slice");
close();
roiManager("Show All");
for ( i=0; i<RoiManager.size; i++ ) {
roiManager("Select",i);
run("Duplicate...","title=#"+(i+1));
run("Clear Outside");
run("Canvas Size...", "width=256 height=256 position=Center zero");
run("Restore Selection");
run("Duplicate...","ignore");
run("8-bit");
run("Fill","slice");
run("Select None");
run("Angular Deviation","noTable");
phi=call("Angular_Deviation.angleReturn");
close();
phi=call("Angular_Deviation.angleReturn");
ref=call("Angular_Deviation.referReturn");
if (ref!="V") phi=90+phi;
run("Select None");
run("Rotate... ","angle=&phi grid=0 interpolation=Bilinear");
selectImage(ttl);
}
run("Select None");
run("Images to Stack", "name=Seeds title=#");
setBatchMode(false);
exit();
//imagej-macro "seeds2stack" (Herbie G., 22. Jan. 2025)
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//imagej-macro "seeds2stack" (Herbie G., 23. Jan. 2025)
//Appproach with"run("Fit Rectangle")" proposed by [email protected]
/*
Requires ImageJ-plugin "RGB_to_CMYK.class"
<https://imagej.net/ij/plugins/cmyk/index.html>
*/
requires("1.54m");
setBackgroundColor(0,0,0);
run("Remove Overlay");
ttl=getTitle();
setBatchMode(true);
run("Duplicate...","title=cpy");
run("RGB to CMYK");
setSlice(2);
setAutoThreshold("Intermodes dark no-reset");
run("Analyze Particles...","add slice");
close();
roiManager("Show All");
n=RoiManager.size;
roiManager("Select",Array.getSequence(n));
roiManager("Combine");
run("Clear Outside");
for ( i=0; i<n;i++ ) {
roiManager("Select",i);
run("Fit Rectangle");
run("Duplicate...","title=#"+(i+1));
run("Rotate 90 Degrees Right");
run("Canvas Size...", "width=128 height=256 position=Center zero");
selectImage("cpy");
}
close("cpy");
selectImage(ttl);
roiManager("Show All");
setBatchMode("exit and display");
run("Images to Stack","name=Seeds title=#");
//setBatchMode(false);
exit();
//imagej-macro "seeds2stack" (Herbie G., 23. Jan. 2025)
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