[Gmod-gbrowse] [Gmod-help] Re: Hi-Res images of conservation tracks have the background turn blue.

Fri May 29 15:56:34 EDT 2009

Mark, Do you see any error_log warnings like "ucsc_glyph: colors will 
be out of sync ($i --> $index)!" ?

Wherever the bad interaction is taking place, it is definitely an 
alpha-channel problem.  To construct the GD::Image using the colormap 
and pixelmap returned by the UCSC C code, 
Bio/Graphics/Glyph/ucsc_glyph.pm uses these calls:

  my $im = GD::Image->new($width, $height);
  $im->transparent( <UCSC colormap's white index> );

... loop on UCSC colormap calls $im->colorAllocate(),
    ** hoping that calling $im->colorAllocate() in the same order
       results in same colormap indices

... loop on UCSC pixelmap calls $im->setPixel()

** Here is where something could go wrong.  It looks like I should 
call $im->transparent *after* the call to $im->colorAllocate() for 
white, making sure that I pass $im's actual white index to 
$im->transparent.  However, when I call transparent after 
colorAllocate, the white pixels are shaded light gray instead of being 
transparent, even in the default display.  Calling $im->transparent 
first was just a hack that worked, and then I forgot about it.  I will 
try updating GD too, to see if that makes any difference.

FWIW I am constructing the GD::Image one color and pixel at a time 
because when I used GD::Image->newFromGdData(), the image was created 
OK but when I returned the new $im from a sub{}, perl crashed with a 
'glibc detected double free or corruption'.  Does that ring a bell for 
anybody?  

Angie

On Fri, 29 May 2009, Todd W. Harris wrote:

> Mark -
> 
> Try upgrading your GD::SVG to the most current version on CPAN.
> 
> Todd
> 
> 
> On May 29, 2009, at 9:42 AM, mark meyer wrote:
> 
> > We use the GD::SVG and was never able to get the inkscape (pdf generation)
> > operational, if that helps any.
> > 
> > On Fri, May 29, 2009 at 9:52 AM, Scott Cain <scott at scottcain.net> wrote:
> > Hi all,
> > 
> > Could this be a bad interaction between the plug in and GD::SVG or
> > inkscape (depending on what sort of hi res image you are getting)?
> > For example, I think that GD::SVG has a hard time with alpha channels.
> > 
> > Scott
> > 
> > 
> > On Fri, May 29, 2009 at 10:31 AM, mark meyer <mmeyerposting at gmail.com>
> > wrote:
> > > Hi Angie,
> > > 
> > > Bill is out of the office today, but I can try to answer your questions.
> > > Attached are the two screen shots, one is what the plugin looks like in
> > > the
> > > gbrowse, just fine as it looks in UCSC.  The second is what happens when
> > > you
> > > click on high-res image.
> > > 
> > > We are running gbrowse v1.69.  The plugin code was implemented and
> > > downloaded about 1 month ago, just recently ran into this issue since we
> > > are
> > > trying to make some publication figures from our Gbrowse data.
> > > 
> > > I can access conf files, etc. if you need to see them and try to do my
> > > best
> > > to answer questions, but I may not be able to answer very detailed
> > > questions
> > > in Bill's absence since he has been the one configuring this.
> > > 
> > > Thanks for checking into this for us,
> > > 
> > > Mark
> > > 
> > > On Thu, May 28, 2009 at 5:29 PM, Angie Hinrichs <angie at soe.ucsc.edu>
> > > wrote:
> > > > 
> > > > Dave - yes, that sounds likely.
> > > > 
> > > > Bill, what version of GBrowse are you running?  How recently did you
> > > > grab the plugin code?  I didn't get the screenshot attachment so if
> > > > you wouldn't mind sending that to me, that would be helpful.  If your
> > > > GBrowse is on a public server, can you send the URL?
> > > > 
> > > > Angie
> > > > 
> > > > On Thu, 28 May 2009, Dave Clements, GMOD Help Desk wrote:
> > > > 
> > > > > Hi Bill,
> > > > >
> > > > > I have no particular insight on why this is happening.  My guess is
> > > > > that it is due some obscure interaction between the UCSC plugin and
> > > > > core GBrowse, but I don't actually know.
> > > > >
> > > > > I've CC'd Angie at UCSC to see if she may have any insight.
> > > > >
> > > > > Dave C.
> > > > >
> > > > >
> > > > >
> > > > > On Tue, May 26, 2009 at 2:25 PM, Bill Pulec <wpulec at gmail.com> wrote:
> > > > > > Hi All,
> > > > > > I am attempting to view high-res images of conservation tracks but
> > > > the
> > > > > > background of these tracks in high-res is blue. This isn't the case
> > > > > > when
> > > > > > these tracks are displayed in gbrowse normally, it only happens when
> > > > > > viewed
> > > > > > as high-res. Also all the non-conservation tracks are fine in high
> > > > > > res. Is
> > > > > > there any reason why outputting these images in high-res would do
> > > > > > this? Has
> > > > > > anyone encountered other tracks doing this in high-res? Any insight
> > > > > > would be
> > > > > > appreciated. I have attached an example image of the track below.
> > > > > >
> > > > > > Thanks,
> > > > > > Bill
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > > Was this helpful?  Let us know at
> > > > > http://gmod.org/wiki/Help_Desk_Feedback
> > > > >
> > > > > Learn more about GMOD at:
> > > > >   SMBE:
> > > > > http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
> > > > >   Arthropod Genomics: http://www.k-state.edu/agc/symp2009/seminar.html
> > > > >   AGA Next Gen Seq in Non-Models:
> > > > > http://www.regonline.com/Nextgeneration
> > > > >
> > > > 
> > > > 
> > > > 
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> > 
> > 
> > 
> > --
> > ------------------------------------------------------------------------
> > Scott Cain, Ph. D.                                   scott at scottcain dot
> > net
> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
> > Ontario Institute for Cancer Research
> > 
> > ------------------------------------------------------------------------------
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