What are the w and h values for a ROI

[Claudia342]

Hi, after I select a region of interest, I have two values for w and h. What are these values for?
w=6.31 (606),  h= 5.06 (486)
Thanks

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[ctrueden]

Hi Claudia,

One is calibrated (i.e., physical dimensions), and the other is in pixels.

See Image > Properties for your image's calibration.
http://imagej.net/docs/guide/146-28.html#sub:Image>Properties...

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Fri, Aug 19, 2016 at 3:41 PM, Claudia342 <[hidden email]>
wrote:

> Hi, after I select a region of interest, I have two values for w and h.
> What are these values for?
> w=6.31 (606),  h= 5.06 (486)
> Thanks
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[PEARSON Matthew]

Hi all,

I was wondering if anyone had any advice on how best to organise a series of macros i have written for easy access by multiple users within ImageJ/Fiji.  Ideally it would be a new menu entry or toolbar icon which produces a drop down list of macros which run when you click an item.  I've had a look at the Menu Tools functionality:
https://imagej.nih.gov/ij/developer/macro/functions.html#newMenu

And seems as if this might do it.  However do i need to have all the code from all the macros contained within the Menu Tool?  I'd prefer to avoid this as it will make it quite bulky and rather i'd prefer some kind of indirect link whereby the Menu Tool simply points to different macros stored in a certain location on the disk and the macro runs when the specific item in the drop down menu is clicked if that is possible?

Thanks for the help,

Matt

--
Matt Pearson
Microscopy Facility
MRC Human Genetics Unit
Institute of Genetics and Molecular Medicine (IGMM)
University of Edinburgh
Crewe Road
EH4 2XU




On 19 Aug 2016, at 21:41, Claudia342 <[hidden email]<mailto:[hidden email]>> wrote:

Hi, after I select a region of interest, I have two values for w and h. What are these values for?
w=6.31 (606),  h= 5.06 (486)
Thanks

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


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The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Kenton Arkill]

I added the following lines after the flood fill macro in the
"StartupMacros.fiji.ijm"
var tCmds = newMenu("Test Menu Tool", newArray("Ser To tif v5","Spread
Rotate v1", "Rotator v2"));
macro "Test Menu Tool -T0b11ET7b09M" {
cmd = getArgument();
run(cmd);
}

To have a menu in the Spare slot (after the flood fill tool) for my 3
common EM macros (in the array)
These marcos are just in the plugins folder (or subfolder)

Regards
Kenton


On 20 September 2016 at 15:55, PEARSON Matthew <
[hidden email]> wrote:

> Hi all,
>
> I was wondering if anyone had any advice on how best to organise a series
> of macros i have written for easy access by multiple users within
> ImageJ/Fiji.  Ideally it would be a new menu entry or toolbar icon which
> produces a drop down list of macros which run when you click an item.  I've
> had a look at the Menu Tools functionality:
> https://imagej.nih.gov/ij/developer/macro/functions.html#newMenu
>
> And seems as if this might do it.  However do i need to have all the code
> from all the macros contained within the Menu Tool?  I'd prefer to avoid
> this as it will make it quite bulky and rather i'd prefer some kind of
> indirect link whereby the Menu Tool simply points to different macros
> stored in a certain location on the disk and the macro runs when the
> specific item in the drop down menu is clicked if that is possible?
>
> Thanks for the help,
>
> Matt
>
> --
> Matt Pearson
> Microscopy Facility
> MRC Human Genetics Unit
> Institute of Genetics and Molecular Medicine (IGMM)
> University of Edinburgh
> Crewe Road
> EH4 2XU
>
>
>
>
> On 19 Aug 2016, at 21:41, Claudia342 <[hidden email]<mailto:
> [hidden email]>> wrote:
>
> Hi, after I select a region of interest, I have two values for w and h.
> What are these values for?
> w=6.31 (606),  h= 5.06 (486)
> Thanks
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Matt,

I don't personally have any great insight into your question, but if
anything nice emerges from this thread, it would make a great topic for the
wiki. Maybe somewhere the "Guides" section of Development? It would come
before http://imagej.net/Distribution -- getting your extensions best
organized.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Tue, Sep 20, 2016 at 9:55 AM, PEARSON Matthew <
[hidden email]> wrote:

> Hi all,
>
> I was wondering if anyone had any advice on how best to organise a series
> of macros i have written for easy access by multiple users within
> ImageJ/Fiji.  Ideally it would be a new menu entry or toolbar icon which
> produces a drop down list of macros which run when you click an item.  I've
> had a look at the Menu Tools functionality:
> https://imagej.nih.gov/ij/developer/macro/functions.html#newMenu
>
> And seems as if this might do it.  However do i need to have all the code
> from all the macros contained within the Menu Tool?  I'd prefer to avoid
> this as it will make it quite bulky and rather i'd prefer some kind of
> indirect link whereby the Menu Tool simply points to different macros
> stored in a certain location on the disk and the macro runs when the
> specific item in the drop down menu is clicked if that is possible?
>
> Thanks for the help,
>
> Matt
>
> --
> Matt Pearson
> Microscopy Facility
> MRC Human Genetics Unit
> Institute of Genetics and Molecular Medicine (IGMM)
> University of Edinburgh
> Crewe Road
> EH4 2XU
>
>
>
>
> On 19 Aug 2016, at 21:41, Claudia342 <[hidden email]<mailto:
> [hidden email]>> wrote:
>
> Hi, after I select a region of interest, I have two values for w and h.
> What are these values for?
> w=6.31 (606),  h= 5.06 (486)
> Thanks
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ved sharma]

Hi Matt,

Why not use ActionBar plugin:

http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:action_bar:start

It does not give you the drop-down list of your macro, but you can create an "Action Bar", with buttons for each your macros. You just have to define each button to the correct address. You can also setup Action Bar to show up automatically every time ImageJ is started.

Ved

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[PEARSON Matthew]

Hi all,

Thanks for the responses, i'll start investigating this.  Kenton, i successfully created a menu item thanks to your code with a drop down list however when i click one of the macros in the list i get an error "Unrecognized command: "name of macro".  I have put the macros in the plugins folder and taken any spaces out of the filename using under-scores.  Any ideas why this might be?

Curtis, it looks like the above might be a good solution but don't know if its broad enough to be a topic on the wiki?

Ved, thanks for the suggestion, I think i'd prefer whichever is the simplest approach and it would be nice if we can just use the imagej toolbar instead of having another toolbar floating on the screen but will look into it.

Thanks,

Matt



--
Matt Pearson
Microscopy Facility
MRC Human Genetics Unit
Institute of Genetics and Molecular Medicine (IGMM)
University of Edinburgh
Crewe Road
EH4 2XU




On 20 Sep 2016, at 15:55, PEARSON Matthew <[hidden email]<mailto:[hidden email]>> wrote:

Hi all,

I was wondering if anyone had any advice on how best to organise a series of macros i have written for easy access by multiple users within ImageJ/Fiji.  Ideally it would be a new menu entry or toolbar icon which produces a drop down list of macros which run when you click an item.  I've had a look at the Menu Tools functionality:
https://imagej.nih.gov/ij/developer/macro/functions.html#newMenu

And seems as if this might do it.  However do i need to have all the code from all the macros contained within the Menu Tool?  I'd prefer to avoid this as it will make it quite bulky and rather i'd prefer some kind of indirect link whereby the Menu Tool simply points to different macros stored in a certain location on the disk and the macro runs when the specific item in the drop down menu is clicked if that is possible?

Thanks for the help,

Matt

--
Matt Pearson
Microscopy Facility
MRC Human Genetics Unit
Institute of Genetics and Molecular Medicine (IGMM)
University of Edinburgh
Crewe Road
EH4 2XU




On 19 Aug 2016, at 21:41, Claudia342 <[hidden email]<mailto:[hidden email]>> wrote:

Hi, after I select a region of interest, I have two values for w and h. What are these values for?
w=6.31 (606),  h= 5.06 (486)
Thanks

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Ryota Homma]

At least in Fiji, a new menu bar entry will appear if you create a new folder under plugins/Scripts/ and put your macros.  

For example, if you put your macros in the folder
Fiji.app/plugins/Scripts/extra/ (assuming you did not change the name of application folder "Fiji.app"),
you will see a new menu entry "extra" in the menu bar.

I don't remember where I learned this feature, but it is working in my copy of Fiji (Windows version).

Best,
Ryota

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[PEARSON Matthew]

Wow that was easy, that might be good enough actually and i could add new menu entries for sets of related macros so long as there weren't too many entries left to right.

Thanks for that,

Matt

--
Matt Pearson
Microscopy Facility
MRC Human Genetics Unit
Institute of Genetics and Molecular Medicine (IGMM)
University of Edinburgh
Crewe Road
EH4 2XU




On 21 Sep 2016, at 16:32, Ryota Homma <[hidden email]<mailto:[hidden email]>> wrote:

At least in Fiji, a new menu bar entry will appear if you create a new folder under plugins/Scripts/ and put your macros.

For example, if you put your macros in the folder
Fiji.app/plugins/Scripts/extra/ (assuming you did not change the name of application folder "Fiji.app"),
you will see a new menu entry "extra" in the menu bar.

I don't remember where I learned this feature, but it is working in my copy of Fiji (Windows version).

Best,
Ryota

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Matt & everyone,

Ryota Homma wrote:

> At least in Fiji, a new menu bar entry will appear if you create a new
> folder under plugins/Scripts/ and put your macros.
>
> For example, if you put your macros in the folder
> Fiji.app/plugins/Scripts/extra/ (assuming you did not change the name
> of application folder "Fiji.app"), you will see a new menu entry
> "extra" in the menu bar.
>
> I don't remember where I learned this feature, but it is working in my
> copy of Fiji (Windows version).

This is a feature of core ImageJ2, which is why it works in Fiji.

As of this writing, the following directories are scanned for scripts (a
macro is a flavor of script):

* scripts
* plugins/Scripts
* plugins

For the technically inclined: you can verify this using the following
Groovy script in the Script Editor:

    // @ScriptService ss
    // @OUTPUT String dirs
    dirs = ss.getScriptDirectories()

Note that the latter two locations (plugins and plugins/Scripts) are
enabled by the ImageJ Legacy component [1] for backwards compatibility. The
canonical best place to put your scripts these days for ImageJ2 is the
"scripts" folder.

Regardless of which place you use, Ryota is right that it will create a
menu structure matching the nested folder structure you use there.

Matthew Pearson wrote:
> Curtis, it looks like the above might be a good solution but don't
> know if its broad enough to be a topic on the wiki?

IMHO, something is better than nothing. Call the page "Organizing
Extensions" or similar, and preface with a statement saying that this page
catalogues some possible nice ways to group and organize related
functionality.

See also this forum thread:

* http://forum.imagej.net/t/customize-menus-in-fiji/2442

There, we discuss our desire to improve the organization of Fiji's menu
structure.

However, I think an "Organizing Extensions" page would be more general and
also talk about other approaches: using the tool bar, shortcut keys in
startup macros, etc.

Regards,
Curtis

[1]
https://github.com/imagej/imagej-legacy/blob/imagej-legacy-0.23.1/src/main/java/net/imagej/legacy/LegacyService.java#L514-L515

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Wed, Sep 21, 2016 at 10:32 AM, Ryota Homma <[hidden email]> wrote:

> At least in Fiji, a new menu bar entry will appear if you create a new
> folder under plugins/Scripts/ and put your macros.
>
> For example, if you put your macros in the folder
> Fiji.app/plugins/Scripts/extra/ (assuming you did not change the name of
> application folder "Fiji.app"),
> you will see a new menu entry "extra" in the menu bar.
>
> I don't remember where I learned this feature, but it is working in my
> copy of Fiji (Windows version).
>
> Best,
> Ryota
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Kenton Arkill]

Thanks Ryota I never new that!

Matt: I don't know, try it with a command you know. It should be whatever
you would write in run("HERE"); in the macro language/recorder.

Best
Kenton

On 21 September 2016 at 17:26, Curtis Rueden <[hidden email]> wrote:

> Hi Matt & everyone,
>
> Ryota Homma wrote:
> > At least in Fiji, a new menu bar entry will appear if you create a new
> > folder under plugins/Scripts/ and put your macros.
> >
> > For example, if you put your macros in the folder
> > Fiji.app/plugins/Scripts/extra/ (assuming you did not change the name
> > of application folder "Fiji.app"), you will see a new menu entry
> > "extra" in the menu bar.
> >
> > I don't remember where I learned this feature, but it is working in my
> > copy of Fiji (Windows version).
>
> This is a feature of core ImageJ2, which is why it works in Fiji.
>
> As of this writing, the following directories are scanned for scripts (a
> macro is a flavor of script):
>
> * scripts
> * plugins/Scripts
> * plugins
>
> For the technically inclined: you can verify this using the following
> Groovy script in the Script Editor:
>
>     // @ScriptService ss
>     // @OUTPUT String dirs
>     dirs = ss.getScriptDirectories()
>
> Note that the latter two locations (plugins and plugins/Scripts) are
> enabled by the ImageJ Legacy component [1] for backwards compatibility. The
> canonical best place to put your scripts these days for ImageJ2 is the
> "scripts" folder.
>
> Regardless of which place you use, Ryota is right that it will create a
> menu structure matching the nested folder structure you use there.
>
> Matthew Pearson wrote:
> > Curtis, it looks like the above might be a good solution but don't
> > know if its broad enough to be a topic on the wiki?
>
> IMHO, something is better than nothing. Call the page "Organizing
> Extensions" or similar, and preface with a statement saying that this page
> catalogues some possible nice ways to group and organize related
> functionality.
>
> See also this forum thread:
>
> * http://forum.imagej.net/t/customize-menus-in-fiji/2442
>
> There, we discuss our desire to improve the organization of Fiji's menu
> structure.
>
> However, I think an "Organizing Extensions" page would be more general and
> also talk about other approaches: using the tool bar, shortcut keys in
> startup macros, etc.
>
> Regards,
> Curtis
>
> [1]
> https://github.com/imagej/imagej-legacy/blob/imagej-
> legacy-0.23.1/src/main/java/net/imagej/legacy/LegacyService.java#L514-L515
>
> --
> Curtis Rueden
> LOCI software architect - http://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Wed, Sep 21, 2016 at 10:32 AM, Ryota Homma <[hidden email]>
> wrote:
>
> > At least in Fiji, a new menu bar entry will appear if you create a new
> > folder under plugins/Scripts/ and put your macros.
> >
> > For example, if you put your macros in the folder
> > Fiji.app/plugins/Scripts/extra/ (assuming you did not change the name of
> > application folder "Fiji.app"),
> > you will see a new menu entry "extra" in the menu bar.
> >
> > I don't remember where I learned this feature, but it is working in my
> > copy of Fiji (Windows version).
> >
> > Best,
> > Ryota
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html