Imshow and Linescan - first version

[Guillaume Gay]

Hi Tony,

Mea culpa, I forgot to attach the code:

I forked sckimage on github and pushed the plugin there:

https://github.com/glyg/scikits-image/blob/master/skimage/io/_plugins/matplotlib_plugin.py

Guillaume

Le 23/02/2012 19:29, Tony Yu a écrit :
>
>
> On Thu, Feb 23, 2012 at 6:22 AM, Guillaume Gay 
> <guillaume at mitotic-machine.org <mailto:guillaume at mitotic-machine.org>> 
> wrote:
>
>     Hi all,
>
>     Here is a first version of the linescan implementation. It sort of
>     works, but I have some issues:
>
>     -the major one is that when I instantiate the LineScanInteractor
>     within the imshow() function definition, I don't catch the events
>     any more. So this is not usable in an interactive session.
>
>     -I can't get the ticks on the linescan plot to update properly...
>
>     -also there should be some kind of a reset mechanism, because if
>     the image is zoomed in, you can lost the handles of the line
>
>     So if any one have a hint on how to do this...
>
>     Meanwhile I can try to have this work in conjunction tifffile's
>     imshow (which should not be so complicated).
>
>     With all that maybe it would be better to implement a subclass of
>     FigureCanvas, so that linescan appears only when a button (at the
>     bottom of the window) is pressed, and it is easy to add e.g. a
>     histogram plot or a contrast setter... what do you think?
>
>
>     Bye
>
>     Guillaume
>
>
> HI Guillaume,
>
> I don't actually see a link or attachment in this email. Could you 
> point me to the code you mention above?
>
> Thanks,
> -Tony
>
>
>     Le 20/02/2012 12:11, Guillaume Gay a écrit :
>
>         Ok, I can give it a try...
>
>         Some questions then:
>
>         - skivi is pure Qt, so must I keep it that way (no matplotlib
>         dependency)?
>         - skivi is good for RGB images, but not so much for
>         greyscale... Also data conversion from uint16 to uint8 turns
>         everything black (it set anything > 256 to 0), shall this be
>         corrected?
>         -Christoph Gohlke tifffile.imshow() is somehow closer to what
>         us microscopy guys are expecting (more suitable for those
>         greyscale multipage tiffs), though some features of the fancy
>         viewer such as the contrast settings, are great. Also it is a
>         pure matplotlib implementation and the intensity value reading
>         is already there. So my question is:
>         Are those tools needed by the general image analysis skimage
>         community are more by scientific tiff users? If the latest, my
>         guess is that building on top of matplotlib and Christoph's
>         implementation of imshow is a better tactic (plus it would be
>         more cross platform, as this can be a widget irrespective of
>         the backend).
>
>         Cheers,
>
>         Guillaume
>
>
>
>
>         Le 20/02/2012 08:04, Stéfan van der Walt a écrit :
>
>             On Fri, Feb 17, 2012 at 6:53 AM, Guillaume Gay
>             <guillaume at mitotic-machine.org
>             <mailto:guillaume at mitotic-machine.org>>  wrote:
>
>                 I just happen to code a simple linescan function, if
>                 that helps...
>
>             Thanks, Guillaume!  If you could integrate this with the
>             fancy Qt
>             imshow to display the line, that would be wonderful, but
>             otherwise I'm
>             sure we'll still be able to use this code.
>
>             Stéfan
>
>
>
>

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