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/matplo... Guillaume Le 23/02/2012 19:29, Tony Yu a écrit :

On Thu, Feb 23, 2012 at 6:22 AM, Guillaume Gay <guillaume@mitotic-machine.org <mailto:guillaume@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@mitotic-machine.org <mailto:guillaume@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