FigureJ Plugin Issue

[Robert Baer]

I really like the new FigureJ Plugin, but have encountered what seems to
be an inconsistency in brightness/contrast behavior. (ImageJ 1.47e)

If one fills several panels with images, on can use the Set Contrast and
brightness to automatically change the display of just the selected
panel, at least at first.  However, I have used the AUTO button and had
all panels adjust at once.  Even this behavior does not happen quite as
consistently as I would expect.  Hitting reset restores all panels to
original, and now several clicks later seems to be when all panels are
suddenly affected by the AUTO button.  I can't quite discern the exact
pattern of how to determine whether one or all panels will be affected,
but my guess is that there is a minor flaw in the selection of Panel(s)
that the brightness and contrast tool works on.

This should be a very helpful tool going forward!  Thanks for sharing it.

  Rob

--
__________________
Robert W. Baer, Ph.D.
Professor of Physiology
Kirksille College of Osteopathic Medicine
A. T. Still University of Health Sciences
Kirksville, MO 63501 USA

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

[Jerome Mutterer-3]

Dear Rob,
Thanks for your comments. The 'Auto' setting in the brightness/contrast
dialog always uses the whole image histogram, and applies the calculated
values to the whole image. The FigureJ figure is a single image so the
behavior of the brightness/contrast dialog is normal.
If you want to adjust B/C setting of a single panel, select this panel, hit
the FigureJ 'open image' button, and this will bring back the original
datasource for this panel. Now you can adjust B/C or any other display
setting, and hitting the 'ok' button again will update the figure panel
accordingly.
Would you like to update the figure pixels directly (example if you
manually paint on a panel with a drawing tool, or after pasting something),
you can do this with the 'options window' 'adopt pixels' button.

Jerome.

On 16 November 2012 01:42, Robert Baer <[hidden email]> wrote:

> I really like the new FigureJ Plugin, but have encountered what seems to
> be an inconsistency in brightness/contrast behavior. (ImageJ 1.47e)
>
> If one fills several panels with images, on can use the Set Contrast and
> brightness to automatically change the display of just the selected panel,
> at least at first.  However, I have used the AUTO button and had all panels
> adjust at once.  Even this behavior does not happen quite as consistently
> as I would expect.  Hitting reset restores all panels to original, and now
> several clicks later seems to be when all panels are suddenly affected by
> the AUTO button.  I can't quite discern the exact pattern of how to
> determine whether one or all panels will be affected, but my guess is that
> there is a minor flaw in the selection of Panel(s) that the brightness and
> contrast tool works on.
>
> This should be a very helpful tool going forward!  Thanks for sharing it.
>
>  Rob
>
> --
> __________________
> Robert W. Baer, Ph.D.
> Professor of Physiology
> Kirksille College of Osteopathic Medicine
> A. T. Still University of Health Sciences
> Kirksville, MO 63501 USA
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>

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

[Robert Baer]

On 11/16/2012 1:31 AM, Jerome Mutterer wrote:

> Dear Rob,
> Thanks for your comments. The 'Auto' setting in the brightness/contrast
> dialog always uses the whole image histogram, and applies the calculated
> values to the whole image. The FigureJ figure is a single image so the
> behavior of the brightness/contrast dialog is normal.
> If you want to adjust B/C setting of a single panel, select this panel, hit
> the FigureJ 'open image' button, and this will bring back the original
> datasource for this panel. Now you can adjust B/C or any other display
> setting, and hitting the 'ok' button again will update the figure panel
> accordingly.
> Would you like to update the figure pixels directly (example if you
> manually paint on a panel with a drawing tool, or after pasting something),
> you can do this with the 'options window' 'adopt pixels' button.
>
> Jerome.

Hi Jerome,

Thanks for the explanation, but I must still be misunderstanding
something.  I have created a 4 panel figure. I click say the lower left
panel.   I open brightness and contrast.  I move the maximum slider, and
only the contrast of the lower left panel is affected. I click the upper
right panel (say) and only the upper right panel is affected when I move
the maximum slider.  At no time have I clicked the 'open image' button
as I would expect to have to do from your feedback.  On the other hand,
if I click AUTO it affects all four images.  Thus, the manual sliders
seem to have a different default target than the AUTO button.  The
manual sliders operate on the selected panel even without 'open image'
whereas the auto button works on the whole FigureJ figure as you suggest
it should.

Your explanation helps me use AUTO with individual panels, but it does
not explain how to use the manual sliders with the whole image or why
they behave differently than the AUTO button with respect to their target.

I must admit to not having gotten as far as drawing tools yet, but I
want to end by again thanking you for this great tool.

Rob

> On 16 November 2012 01:42, Robert Baer <[hidden email]> wrote:
>
>> I really like the new FigureJ Plugin, but have encountered what seems to
>> be an inconsistency in brightness/contrast behavior. (ImageJ 1.47e)
>>
>> If one fills several panels with images, on can use the Set Contrast and
>> brightness to automatically change the display of just the selected panel,
>> at least at first.  However, I have used the AUTO button and had all panels
>> adjust at once.  Even this behavior does not happen quite as consistently
>> as I would expect.  Hitting reset restores all panels to original, and now
>> several clicks later seems to be when all panels are suddenly affected by
>> the AUTO button.  I can't quite discern the exact pattern of how to
>> determine whether one or all panels will be affected, but my guess is that
>> there is a minor flaw in the selection of Panel(s) that the brightness and
>> contrast tool works on.
>>
>> This should be a very helpful tool going forward!  Thanks for sharing it.
>>
>>   Rob
>>
>> --
>> __________________
>> Robert W. Baer, Ph.D.
>> Professor of Physiology
>> Kirksille College of Osteopathic Medicine
>> A. T. Still University of Health Sciences
>> Kirksville, MO 63501 USA
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
__________________
Robert W. Baer, Ph.D.
Professor of Physiology
Kirksille College of Osteopathic Medicine
A. T. Still University of Health Sciences
Kirksville, MO 63501 USA

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

[edda zinck]

hi rob,

it is generally a bad idea to change *pixels* manually in the figure window!
changes done there by something ore somebody else than figureJ itself
internally *are not permanently stored**.
if you drag the separators (white lines between panels) after doing your
brightness/contrast adjusting, the effect will be gone.
also if you save and re-open the file, your changes might have disappeared.

this is becaus the task of the figure window is:
-> layout ajustment
-> labeling

layout changement is done in the main figure window.
image appearence changes have to be done in the window that opens when you
hit "open image", as this window is responsible to *prepare the image pixels
* for presentation on the panel.

thus, your workflow should be:
-> layout creation
-> select a panel
-> hit "open image"
-> use the selection tool to select the part you want to display in your
panel
-> adjust brightness and contrast
-> hit "ok"

this
a) logs the brightness-contrast changing to your log file
b) permanently stores your adjusted pixels in your panel



please try to keep with this workflow :)



kind regards,

edda


* if you can't avoid to change the pixels for some reason, you can go to
the ´"options" -> "adopt pixels button"
then they are stored permanently.
this is not necessary for objects that are on the overlay. we keep track of
them :)



On 16 November 2012 15:42, Robert Baer <[hidden email]> wrote:

> On 11/16/2012 1:31 AM, Jerome Mutterer wrote:
>
>> Dear Rob,
>> Thanks for your comments. The 'Auto' setting in the brightness/contrast
>> dialog always uses the whole image histogram, and applies the calculated
>> values to the whole image. The FigureJ figure is a single image so the
>> behavior of the brightness/contrast dialog is normal.
>> If you want to adjust B/C setting of a single panel, select this panel,
>> hit
>> the FigureJ 'open image' button, and this will bring back the original
>> datasource for this panel. Now you can adjust B/C or any other display
>> setting, and hitting the 'ok' button again will update the figure panel
>> accordingly.
>> Would you like to update the figure pixels directly (example if you
>> manually paint on a panel with a drawing tool, or after pasting
>> something),
>> you can do this with the 'options window' 'adopt pixels' button.
>>
>> Jerome.
>>
> Hi Jerome,
>
> Thanks for the explanation, but I must still be misunderstanding
> something.  I have created a 4 panel figure. I click say the lower left
> panel.   I open brightness and contrast.  I move the maximum slider, and
> only the contrast of the lower left panel is affected. I click the upper
> right panel (say) and only the upper right panel is affected when I move
> the maximum slider.  At no time have I clicked the 'open image' button as I
> would expect to have to do from your feedback.  On the other hand, if I
> click AUTO it affects all four images.  Thus, the manual sliders seem to
> have a different default target than the AUTO button.  The manual sliders
> operate on the selected panel even without 'open image' whereas the auto
> button works on the whole FigureJ figure as you suggest it should.
>
> Your explanation helps me use AUTO with individual panels, but it does not
> explain how to use the manual sliders with the whole image or why they
> behave differently than the AUTO button with respect to their target.
>
> I must admit to not having gotten as far as drawing tools yet, but I want
> to end by again thanking you for this great tool.
>
> Rob
>
>  On 16 November 2012 01:42, Robert Baer <[hidden email]> wrote:
>>
>>  I really like the new FigureJ Plugin, but have encountered what seems to
>>> be an inconsistency in brightness/contrast behavior. (ImageJ 1.47e)
>>>
>>> If one fills several panels with images, on can use the Set Contrast and
>>> brightness to automatically change the display of just the selected
>>> panel,
>>> at least at first.  However, I have used the AUTO button and had all
>>> panels
>>> adjust at once.  Even this behavior does not happen quite as consistently
>>> as I would expect.  Hitting reset restores all panels to original, and
>>> now
>>> several clicks later seems to be when all panels are suddenly affected by
>>> the AUTO button.  I can't quite discern the exact pattern of how to
>>> determine whether one or all panels will be affected, but my guess is
>>> that
>>> there is a minor flaw in the selection of Panel(s) that the brightness
>>> and
>>> contrast tool works on.
>>>
>>> This should be a very helpful tool going forward!  Thanks for sharing it.
>>>
>>>   Rob
>>>
>>> --
>>> __________________
>>> Robert W. Baer, Ph.D.
>>> Professor of Physiology
>>> Kirksille College of Osteopathic Medicine
>>> A. T. Still University of Health Sciences
>>> Kirksville, MO 63501 USA
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.****html<http://imagej.nih.gov/ij/list.**html>
>>> <http://imagej.nih.gov/**ij/list.html<http://imagej.nih.gov/ij/list.html>
>>> >
>>>
>>>  --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>
>
>
> --
> __________________
> Robert W. Baer, Ph.D.
> Professor of Physiology
> Kirksille College of Osteopathic Medicine
> A. T. Still University of Health Sciences
> Kirksville, MO 63501 USA
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>

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