TrakEM2: save area list name in the result window

[Luisa de Vivo]

TrakEM2 users,

I'm segmenting and reconstructing different objects with TrakEM2, in order
to measure volumes of all the area lists that I have in my project.
Unfortunately, when I look at the result window, the area lists are
identified only by the number that TrakEM2 assigns to them.
Is there a way to control a priori, and possibly change, how TrakEM2
assigns the number that identify the area lists?
Alternatively, is there a way to save in the result window the name I gave
to a specific area list (with the rename command)?
This would be helpful later for data processing.
Thank you very much.

Luisa


--
Luisa de Vivo, PhD
Department of Psychiatry
University of Wisconsin
6001 Research Park Boulevard
Madison WI 53719

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[Albert Cardona-2]

2013/4/4 Luisa de Vivo <[hidden email]>

> TrakEM2 users,
>
> I'm segmenting and reconstructing different objects with TrakEM2, in order
> to measure volumes of all the area lists that I have in my project.
> Unfortunately, when I look at the result window, the area lists are
> identified only by the number that TrakEM2 assigns to them.
> Is there a way to control a priori, and possibly change, how TrakEM2
> assigns the number that identify the area lists?
> Alternatively, is there a way to save in the result window the name I gave
> to a specific area list (with the rename command)?
> This would be helpful later for data processing.
> Thank you very much.
>
> Luisa
>

Hi Luisa,

The results window only allows, as far as I know, a single text column.
Would love to write the name in there but if I recall correctly I chose to
write the units instead. Also, names could be repeated, so the ID prevents
confusion when two arealists have been assigned the same name.

Wayne, Johannes, Curtis: is there a way to add String-containing columns to
a ResultsTable in ImageJ?

Luisa: to solve your issue, you could export a table of arealist ID vs
arealist name. Open the Script Editor (File - New - Script), choose the
python language (Languages - Python) and then paste the following and push
the "Run" button:

###
from ini.trakem2.display import AreaList, Display
arealists = Display.getFront().getLayerSet().getZDisplayables(AreaList)
for arealist in arealists:
    print arealist.getId(), "--", arealist.getTitle(), "--",
arealist.getProject().getShortMeaningfulTitle(arealist)

###

The third element printed, the "getShortMeaningfulTitle()", will print the
name of the parent element in the Project Tree. For example, if you have an
abstract node of type "neuron" and you gave it the name "CA1", and it
contained an unnamed arealist, then the CA1 name will be printed.

See also:
http://fiji.sc/TrakEM2_Scripting

Albert Cardona

--
http://albert.rierol.net
http://www.ini.uzh.ch/~acardona/

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[dscho]

Hi Albert,

On Thu, 4 Apr 2013, Albert Cardona wrote:

> Wayne, Johannes, Curtis: is there a way to add String-containing columns
> to a ResultsTable in ImageJ?

No. You can make column headings or row labels. But you cannot set
ResultsTables' values to anything else than doubles. And changing things
now would break numerous existing (and so-far working) plugins.

What you *can* do, though, is follow this example to use an IJ2 results
table in TrakEM2:

        https://groups.google.com/forum/?fromgroups=#!topic/fiji-devel/eJcedexen0Q

It is very easy, now that TrakEM2 is Mavenized. BTW have you seen my pull
request? https://github.com/fiji/TrakEM2/pull/3

Ciao,
Johannes

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

[Albert Cardona-2]

2013/4/4 Johannes Schindelin <[hidden email]>

> Hi Albert,
>
> On Thu, 4 Apr 2013, Albert Cardona wrote:
>
> > Wayne, Johannes, Curtis: is there a way to add String-containing columns
> > to a ResultsTable in ImageJ?
>
> No. You can make column headings or row labels. But you cannot set
> ResultsTables' values to anything else than doubles. And changing things
> now would break numerous existing (and so-far working) plugins.
>
> What you *can* do, though, is follow this example to use an IJ2 results
> table in TrakEM2:
>
>
> https://groups.google.com/forum/?fromgroups=#!topic/fiji-devel/eJcedexen0Q
>
> It is very easy, now that TrakEM2 is Mavenized. BTW have you seen my pull
> request? https://github.com/fiji/TrakEM2/pull/3
>
> Ciao,
> Johannes
>

Thanks Johannes! Will look into it.

On the pull request: merged it. Thanks!

Albert


--
http://albert.rierol.net
http://www.ini.uzh.ch/~acardona/

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[Luisa de Vivo]

Thank you for your suggestions. I was able to get the list of area list
names and id printed with Albert's script, I'll look also into the IJ2
result table.
Thanks.
Luisa


On Thu, Apr 4, 2013 at 8:22 PM, Albert Cardona <[hidden email]> wrote:

> 2013/4/4 Johannes Schindelin <[hidden email]>
>
> > Hi Albert,
> >
> > On Thu, 4 Apr 2013, Albert Cardona wrote:
> >
> > > Wayne, Johannes, Curtis: is there a way to add String-containing
> columns
> > > to a ResultsTable in ImageJ?
> >
> > No. You can make column headings or row labels. But you cannot set
> > ResultsTables' values to anything else than doubles. And changing things
> > now would break numerous existing (and so-far working) plugins.
> >
> > What you *can* do, though, is follow this example to use an IJ2 results
> > table in TrakEM2:
> >
> >
> >
> https://groups.google.com/forum/?fromgroups=#!topic/fiji-devel/eJcedexen0Q
> >
> > It is very easy, now that TrakEM2 is Mavenized. BTW have you seen my pull
> > request? https://github.com/fiji/TrakEM2/pull/3
> >
> > Ciao,
> > Johannes
> >
>
>
>
> Thanks Johannes! Will look into it.
>
> On the pull request: merged it. Thanks!
>
> Albert
>
>
> --
> http://albert.rierol.net
> http://www.ini.uzh.ch/~acardona/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Luisa de Vivo, PhD
Department of Psychiatry
University of Wisconsin
6001 Research Park Boulevard
Madison WI 53719

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

[Rasband, Wayne (NIH/NIMH) [E]]

On Apr 4, 2013, at 5:25 PM, Albert Cardona wrote:

> 2013/4/4 Luisa de Vivo <[hidden email]>
>
>> TrakEM2 users,
>>
>> I'm segmenting and reconstructing different objects with TrakEM2, in order
>> to measure volumes of all the area lists that I have in my project.
>> Unfortunately, when I look at the result window, the area lists are
>> identified only by the number that TrakEM2 assigns to them.
>> Is there a way to control a priori, and possibly change, how TrakEM2
>> assigns the number that identify the area lists?
>> Alternatively, is there a way to save in the result window the name I gave
>> to a specific area list (with the rename command)?
>> This would be helpful later for data processing.
>> Thank you very much.
>>
>> Luisa
>>
>
>
> Hi Luisa,
>
> The results window only allows, as far as I know, a single text column.
> Would love to write the name in there but if I recall correctly I chose to
> write the units instead. Also, names could be repeated, so the ID prevents
> confusion when two arealists have been assigned the same name.
>
> Wayne, Johannes, Curtis: is there a way to add String-containing columns to
> a ResultsTable in ImageJ?

Results tables in ImageJ 1.47o, due in about two weeks, will support multiple string columns.

-wayne

> Luisa: to solve your issue, you could export a table of arealist ID vs
> arealist name. Open the Script Editor (File - New - Script), choose the
> python language (Languages - Python) and then paste the following and push
> the "Run" button:
>
> ###
> from ini.trakem2.display import AreaList, Display
> arealists = Display.getFront().getLayerSet().getZDisplayables(AreaList)
> for arealist in arealists:
>    print arealist.getId(), "--", arealist.getTitle(), "--",
> arealist.getProject().getShortMeaningfulTitle(arealist)
>
> ###
>
> The third element printed, the "getShortMeaningfulTitle()", will print the
> name of the parent element in the Project Tree. For example, if you have an
> abstract node of type "neuron" and you gave it the name "CA1", and it
> contained an unnamed arealist, then the CA1 name will be printed.
>
> See also:
> http://fiji.sc/TrakEM2_Scripting
>
> Albert Cardona
>
> --
> http://albert.rierol.net
> http://www.ini.uzh.ch/~acardona/

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