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

Mon Jun 1 13:59:13 EDT 2009

That's good news.

Lincoln

On Mon, Jun 1, 2009 at 1:57 PM, Angie Hinrichs <angie at soe.ucsc.edu> wrote:

> Thanks!  I just checked that in to CVS -- the external repository
> should be updated by noon Pacific time.  The light blue lines go away
> but at least the track image doesn't disappear into dark blue.  :)
>
> Angie
>
> On Mon, 1 Jun 2009, Lincoln Stein wrote:
>
> > Hi Angie,
> >
> > Try this: if ($gd->isa('GD::SVG')) { # in high res mode }
> >
> > Lincoln
> >
> > On Mon, Jun 1, 2009 at 12:57 PM, Angie Hinrichs <angie at soe.ucsc.edu>
> wrote:
> >
> > > I took a look at the latest C source code for gdImageCopy()
> > > (
> http://cvs.php.net/viewvc.cgi/gd/libgd/src/gd.c?revision=1.83&view=markup
> > > )
> > > and it looks like since gd version 2.0.10, if a pixel is transparent
> > > in the source, it is not copied to the destination.  I can see how
> > > that might interact badly when copying into something other than
> > > another pixellated image.
> > >
> > > Is there a hook in GBrowse by which a plugin or glyph can tell that it
> > > is in high-res mode, so it can avoid using transparency?
> > >
> > > Thanks,
> > > Angie
> > >
> > > On Fri, 29 May 2009, Lincoln Stein wrote:
> > >
> > > > Ok. I'll poke around in GD::SVG to see what might be the problem with
> > > this
> > > > strategy. It ought to be ok.
> > > >
> > > > Lincoln
> > > >
> > > > On Fri, May 29, 2009 at 5:18 PM, Angie Hinrichs <angie at soe.ucsc.edu>
> > > wrote:
> > > >
> > > > > > Angie, is there any reason to call transparent()? The other
> tracks
> > > render
> > > > > > their background in a solid color.
> > > > >
> > > > > In a nutshell, to avoid hiding the vertical light blue ruler lines
> in
> > > > > the background by drawing white on top of them.
> > > > >
> > > > > Currently, ucsc_glyph::draw gets a colormap+pixelmap representation
> of
> > > > > an image with a white background (from UCSC C code by way of
> > > > > UcscConservation plugin), creates a GD::Image $im as described
> below
> > > > > and uses $gd->copy to plop that on top of the GBrowse image:
> > > > >
> > > > >  $gd->copy($im, $x-$leftLabelWidth, $y, 0, 0, $width, $height);
> > > > >
> > > > > -- so it bypasses all of the usual glyph draw() infrastructure, and
> > > > > renders the entire allocated space in the main image.  Using
> > > > > transparency preserves the light blue lines and whatever else might
> be
> > > > > in the background... is it not worth the trouble?  Is there a
> better
> > > > > way?
> > > > >
> > > > > Thanks,
> > > > > Angie
> > > > >
> > > > > On Fri, 29 May 2009, Lincoln Stein wrote:
> > > > >
> > > > > > Angie, is there any reason to call transparent()? The other
> tracks
> > > render
> > > > > > their background in a solid color.
> > > > > >
> > > > > > Lincoln
> > > > > >
> > > > > > On Fri, May 29, 2009 at 3:56 PM, Angie Hinrichs <
> angie at soe.ucsc.edu>
> > > > > wrote:
> > > > > >
> > > > > > > Mark, Do you see any error_log warnings like "ucsc_glyph:
> colors
> > > will
> > > > > > > be out of sync ($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
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-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
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