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Random points in a stack

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AAM71

Random points in a stack

Dear All,
For one of my small macro projects in counting I need to generate random
points in a stack and use Multi-point tool to count them. I need two
variants: 1) each stack slice contains its own points; 2) all slices
contain the same set of points - points on the first slice are seen
through all of them. I have tried 2 methods: makePoint() and
makeSelection(). Both are not good enough. makePoint allows to change
properties of points and works well with Multi-point Tool but creates
only the 1st variant (separate set for each slice). makeSelection
creates the 2nd variant but does not allow to change point properties
(color, size etc.) and does not work very well with Multi-point Tool.
Are there workarounds for that? I do not see Overlay options for points
(like Overlay.drawLine that I have used in my precious macros
successfully).
Example macros are attached.

--
Sincerely,
Alex

macro1---------------------
run("MRI Stack (528K)");
getDimensions(width, height, channels, slices, frames);
PntNumber = 5;
for (i=0; i<PntNumber; i++) {
         x = round(random*(width-1));
         y = round(random*(height-1));
         makePoint(x, y, "small red cross add");
};
--------------------------

macro2-------------------

run("MRI Stack (528K)");
getDimensions(width, height, channels, slices, frames);
PntNumber = 5;
for (i=0; i<PntNumber; i++) {
         x = newArray(PntNumber);
         y = newArray(PntNumber);
         for (i=0; i<x.length; i++) {
             x[i] = round(random*(width-1));
         }
         for (i=0; i<x.length; i++) {
             y[i] = round(random*(height-1));
         }
         makeSelection("point", x, y);
};
--------------------

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Wayne Rasband-2

Re: Random points in a stack

> On Nov 5, 2018, at 10:29 AM, Aleksandr Mironov <[hidden email]> wrote:
>
> Dear All,
> For one of my small macro projects in counting I need to generate random points in a stack and use Multi-point tool to count them. I need two variants: 1) each stack slice contains its own points; 2) all slices contain the same set of points - points on the first slice are seen through all of them. I have tried 2 methods: makePoint() and makeSelection(). Both are not good enough. makePoint allows to change properties of points and works well with Multi-point Tool but creates only the 1st variant (separate set for each slice).

Points created by makePoint() will appear in all slices if you set the positions to 0, as in this example:

run("MRI Stack (528K)");
getDimensions(width, height, channels, slices, frames);
PntNumber = 5;
for (i=0; i<PntNumber; i++) {
x = round(random*(width-1));
y = round(random*(height-1));
makePoint(x, y, "large cyan cross add");
Overlay.setPosition(0);
};

> makeSelection creates the 2nd variant but does not allow to change point properties (color, size etc.) and does not work very well with Multi-point Tool.

You can set point properties (color, size etc.) with makeSelection() in the same way as makePoint(), as in this example:

run("MRI Stack (528K)");
getDimensions(width, height, channels, slices, frames);
PntNumber = 5;
for (i=0; i<PntNumber; i++) {
x = newArray(PntNumber);
y = newArray(PntNumber);
for (i=0; i<x.length; i++)
x[i] = round(random*(width-1));
for (i=0; i<x.length; i++)
y[i] = round(random*(height-1));
makeSelection("large cyan cross points", x, y);
}

-wayne

> Are there workarounds for that? I do not see Overlay options for points (like Overlay.drawLine that I have used in my precious macros successfully).
> Example macros are attached.
>
> --
> Sincerely,
> Alex
>
>
> macro1---------------------
> run("MRI Stack (528K)");
> getDimensions(width, height, channels, slices, frames);
> PntNumber = 5;
> for (i=0; i<PntNumber; i++) {
> x = round(random*(width-1));
> y = round(random*(height-1));
> makePoint(x, y, "small red cross add");
> };
> --------------------------
>
> macro2-------------------
>
> run("MRI Stack (528K)");
> getDimensions(width, height, channels, slices, frames);
> PntNumber = 5;
> for (i=0; i<PntNumber; i++) {
> x = newArray(PntNumber);
> y = newArray(PntNumber);
> for (i=0; i<x.length; i++) {
> x[i] = round(random*(width-1));
> }
> for (i=0; i<x.length; i++) {
> y[i] = round(random*(height-1));
> }
> makeSelection("point", x, y);
> };

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AAM71

Re: Random points in a stack

Thank you Wayne!

Sincerely,

Alex

On 06/11/2018 05:21, Wayne Rasband wrote:

>> On Nov 5, 2018, at 10:29 AM, Aleksandr Mironov <[hidden email]> wrote:
>>
>> Dear All,
>> For one of my small macro projects in counting I need to generate random points in a stack and use Multi-point tool to count them. I need two variants: 1) each stack slice contains its own points; 2) all slices contain the same set of points - points on the first slice are seen through all of them. I have tried 2 methods: makePoint() and makeSelection(). Both are not good enough. makePoint allows to change properties of points and works well with Multi-point Tool but creates only the 1st variant (separate set for each slice).
> Points created by makePoint() will appear in all slices if you set the positions to 0, as in this example:
>
> run("MRI Stack (528K)");
> getDimensions(width, height, channels, slices, frames);
> PntNumber = 5;
> for (i=0; i<PntNumber; i++) {
> x = round(random*(width-1));
> y = round(random*(height-1));
> makePoint(x, y, "large cyan cross add");
> Overlay.setPosition(0);
> };
>
>> makeSelection creates the 2nd variant but does not allow to change point properties (color, size etc.) and does not work very well with Multi-point Tool.
> You can set point properties (color, size etc.) with makeSelection() in the same way as makePoint(), as in this example:
>
> run("MRI Stack (528K)");
> getDimensions(width, height, channels, slices, frames);
> PntNumber = 5;
> for (i=0; i<PntNumber; i++) {
> x = newArray(PntNumber);
> y = newArray(PntNumber);
> for (i=0; i<x.length; i++)
> x[i] = round(random*(width-1));
> for (i=0; i<x.length; i++)
> y[i] = round(random*(height-1));
> makeSelection("large cyan cross points", x, y);
> }
>
> -wayne
>
>
>> Are there workarounds for that? I do not see Overlay options for points (like Overlay.drawLine that I have used in my precious macros successfully).
>> Example macros are attached.
>>
>> --
>> Sincerely,
>> Alex
>>
>>
>> macro1---------------------
>> run("MRI Stack (528K)");
>> getDimensions(width, height, channels, slices, frames);
>> PntNumber = 5;
>> for (i=0; i<PntNumber; i++) {
>> x = round(random*(width-1));
>> y = round(random*(height-1));
>> makePoint(x, y, "small red cross add");
>> };
>> --------------------------
>>
>> macro2-------------------
>>
>> run("MRI Stack (528K)");
>> getDimensions(width, height, channels, slices, frames);
>> PntNumber = 5;
>> for (i=0; i<PntNumber; i++) {
>> x = newArray(PntNumber);
>> y = newArray(PntNumber);
>> for (i=0; i<x.length; i++) {
>> x[i] = round(random*(width-1));
>> }
>> for (i=0; i<x.length; i++) {
>> y[i] = round(random*(height-1));
>> }
>> makeSelection("point", x, y);
>> };
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Cammer, Michael-2

Re: Random points in a stack

In reply to this post by Wayne Rasband-2

These are very useful additions to selections. Thank you for adding them.
Are there other great functionalities we are missing? Unfortunately, these (the setting to zero and other options) aren't documented at https://imagej.nih.gov/ij/developer/macro/functions.html or https://imagej.nih.gov/ij/macros/MakeSelectionDemo.txt
Best regards-

Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory
NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY 10016
C: 914-309-3270 [hidden email] http://nyulmc.org/micros http://microscopynotes.com/

-----Original Message-----
From: Wayne Rasband <[hidden email]>
Sent: Tuesday, November 6, 2018 12:21 AM
To: [hidden email]
Subject: Re: Random points in a stack

Points created by makePoint() will appear in all slices if you set the positions to 0, as in this example:

run("MRI Stack (528K)");
getDimensions(width, height, channels, slices, frames);
PntNumber = 5;
for (i=0; i<PntNumber; i++) {
x = round(random*(width-1));
y = round(random*(height-1));
makePoint(x, y, "large cyan cross add");
Overlay.setPosition(0);
};

You can set point properties (color, size etc.) with makeSelection() in the same way as makePoint(), as in this example:

run("MRI Stack (528K)");
getDimensions(width, height, channels, slices, frames);
PntNumber = 5;
for (i=0; i<PntNumber; i++) {
x = newArray(PntNumber);
y = newArray(PntNumber);
for (i=0; i<x.length; i++)
x[i] = round(random*(width-1));
for (i=0; i<x.length; i++)
y[i] = round(random*(height-1));
makeSelection("large cyan cross points", x, y);
}

-wayne

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AAM71

Re: Random points in a stack

In reply to this post by Wayne Rasband-2

Dear Wayne,

I have found small niggle when I tried to use makePoint() in my macro:

newImage("New", "8-bit ramp", 512, 512, 1);

makePoint(200, 200, "large red cross add");
Overlay.setPosition(0);

Two colors (green and orange) do not work with this macro, making the
point yellow (default) instead of green or orange. If I try to make
points manually (Point Tool) and choosing color by double click then
these colors work fine.

Sincerely,

Alex

On 06/11/2018 05:21, Wayne Rasband wrote:

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