save Console window text to a file?

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save Console window text to a file?

Kenneth R Sloan-2
I'm trying to remotely debug a FIJI configuration issue (remote, as in: 7 time zones).

The user's FIJI writes a couple of pages of stderr output to the Console window when FIJI is
started.  All I have right now is a fragmentary screen shot, which implicates:

        java.util.regex.Patt...

among other things.

I asked for the full contents of the Console window - but realized that I don't know how to save the Console text.  On my machine, when I make the Console window current there is no "save as" menu option (just Fiji and Edit).

Looking at somewhat relevant queries online, it looks like I can write a macro to save the Console window - but I'd much prefer to be able to do it directly in the interface.  (remember, I won't be doing it - I have to explain this to the user).

What am I missing?  Are the Console contents written to some  "well known filename" that I don't know about?

--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.

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Re: save Console window text to a file?

Curtis Rueden-2
Hi Kenneth,

> I asked for the full contents of the Console window - but realized
> that I don't know how to save the Console text.  On my machine, when I
> make the Console window current there is no "save as" menu option
> (just Fiji and Edit).

Is Ctrl+A to select all, then Ctrl+C to copy to clipboard a viable option
for you?

(There is also a ConsoleListener API to hook into the console events, but
you're just looking for an easy way to grab the text out of there from the
UI, right?)

Regards,
Curtis

--
Curtis Rueden
Software architect, LOCI/Eliceiri lab - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Have you tried the Image.sc Forum? https://forum.image.sc/



On Fri, Dec 11, 2020 at 3:31 PM Kenneth Sloan <[hidden email]>
wrote:

> I'm trying to remotely debug a FIJI configuration issue (remote, as in: 7
> time zones).
>
> The user's FIJI writes a couple of pages of stderr output to the Console
> window when FIJI is
> started.  All I have right now is a fragmentary screen shot, which
> implicates:
>
>         java.util.regex.Patt...
>
> among other things.
>
> I asked for the full contents of the Console window - but realized that I
> don't know how to save the Console text.  On my machine, when I make the
> Console window current there is no "save as" menu option (just Fiji and
> Edit).
>
> Looking at somewhat relevant queries online, it looks like I can write a
> macro to save the Console window - but I'd much prefer to be able to do it
> directly in the interface.  (remember, I won't be doing it - I have to
> explain this to the user).
>
> What am I missing?  Are the Console contents written to some  "well known
> filename" that I don't know about?
>
> --
> Kenneth Sloan
> [hidden email]
> Vision is the art of seeing what is invisible to others.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Regroup two pieces of images

vu long tran
Dear all,

I am using imagej to process my histological images. I would like to join two pieces of tissues that unfortunately fell apart during the cryo-sectioning process. I could use either GIMP or TrakEM2 to put them together. However, GIMP could not recognize 16 bit images. I would like to keep it at 16 bit since I have several others which are in 16-bit. With TrakEM2, I need to remove the background color. But I could not find a function to add an alpha channel in ImageJ as in GIMP to help me really clear it. I can blend them together but the intensity will be reduced and become hard to compare with other sections.
I hope someone can give me the suggestions to solve this problem.

Thank you all for your time
Best regards,


Vu-Long Tran

PhD, Postdoctoral Researcher

Laboratory of In Vivo Molecular Imaging (IMIV)
CEA/Institute of Life Sciences/Hospital Service Frédéric Joliot

UMR 1023 Inserm/CEA/Université Paris Sud - ERL 9218 CNRS
4 place du Général Leclerc
91400 Orsay
Tel. office: 01 69 86 77 69
Portable: 07 53 88 24 07



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Re: Regroup two pieces of images

Michael Schmid
Hi Vu-Long,

there is an Alpha Channel plugin that might do what you need. It works
for 16-bit images, but the alpha channel must be 8 bits or float (32 bits).
   https://imagejdocu.tudor.lu/plugin/utilities/alpha_channel/start

How to use it:
- The alpha channel and the target image must have the same number of
pixels in x&y.
- It is advisable to have the “Keep multiple undo buffers” option
enabled in Edit>Options>Memory & Threads
- Copy the whole source image and paste it on the target image
- Then call the Alpha Channel plugin; use 'preview' to see the result.
The plugin allows you to modify the alpha channel, e.g. for smoother
boundaries or shrink/enlarge it a few pixels.

Michael
__________________________________________________________________________


On 16/12/2020 6:01 pm, vu long tran wrote:

> Dear all,
>
> I am using imagej to process my histological images. I would like to join two pieces of tissues that unfortunately fell apart during the cryo-sectioning process. I could use either GIMP or TrakEM2 to put them together. However, GIMP could not recognize 16 bit images. I would like to keep it at 16 bit since I have several others which are in 16-bit. With TrakEM2, I need to remove the background color. But I could not find a function to add an alpha channel in ImageJ as in GIMP to help me really clear it. I can blend them together but the intensity will be reduced and become hard to compare with other sections.
> I hope someone can give me the suggestions to solve this problem.
>
> Thank you all for your time
> Best regards,
>
>
> Vu-Long Tran
>
> PhD, Postdoctoral Researcher
>
> Laboratory of In Vivo Molecular Imaging (IMIV)
> CEA/Institute of Life Sciences/Hospital Service Frédéric Joliot
>

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