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

Bill Pulec wpulec at gmail.com
Mon Jun 1 15:39:49 EDT 2009 

The new CVS checkout works!

Thanks a lot,
Bill

On Mon, Jun 1, 2009 at 12:59 PM, Lincoln Stein <lstein at cshl.edu> wrote:

> 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
>> > > > > > > > > > > >
>> > > > > > > > > > >
>> > > > > > > > > > >
>> > > > > > > > > > >
>> > > > > > > > > > >
>> > > > > > >
>> > > > >
>> > >
>> ------------------------------------------------------------------------------
>> > > > > > > > > > > Register Now for Creativity and Technology (CaT), June
>> 3rd,
>> > > > > NYC.
>> > > > > > > CaT
>> > > > > > > > > > > is a gathering of tech-side developers & brand
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>> > > > > > > professionals.
>> > > > > > > > > > > Meet
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>> > > > > like
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>> > > > > > > > > > > Group, R/GA, & Big Spaceship.
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>> > > > > > > > > > > _______________________________________________
>> > > > > > > > > > > Gmod-gbrowse mailing list
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>> > > > > > > > > > >
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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
>> > > > > > > > >
>> > > > > > > > >
>> > > > > > >
>> > > > >
>> > >
>> ------------------------------------------------------------------------------
>> > > > > > > > > Register Now for Creativity and Technology (CaT), June
>> 3rd,
>> > > NYC.
>> > > > > CaT
>> > > > > > > > > is a gathering of tech-side developers & brand creativity
>> > > > > > > professionals.
>> > > > > > > > > Meet
>> > > > > > > > > the minds behind Google Creative Lab, Visual Complexity,
>> > > > > Processing, &
>> > > > > > > > > iPhoneDevCamp as they present alongside digital
>> heavyweights
>> > > like
>> > > > > > > Barbarian
>> > > > > > > > > Group, R/GA, & Big Spaceship.
>> > > > > http://p.sf.net/sfu/creativitycat-com
>> > > > > > > > > _______________________________________________
>> > > > > > > > > Gmod-gbrowse mailing list
>> > > > > > > > > Gmod-gbrowse at lists.sourceforge.net
>> > > > > > > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> > > > > > > >
>> > > > > > >
>> > > > > >
>> > > > > >
>> > > > > >
>> > > > > >
>> > > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > >
>> >
>> >
>> >
>> >
>>
>
>
>
> --
> 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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