« Return to Thread: Hi-Res images of conservation tracks have the background turn blue.
Re: [Gmod-help] Re: Hi-Res images of conservation tracks have the background turn blue.
by Angie Hinrichs
::
Rate this Message:
> 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, $height);
-- so it bypasses all of the usual glyph draw() infrastructure, and
renders the entire allocated space in the main image. Using
transparency preserves the light blue lines and whatever else might be
in the background... is it not worth the trouble? Is there a better
way?
Thanks,
Angie
On Fri, 29 May 2009, Lincoln Stein wrote:
> Angie, is there any reason to call transparent()? The other tracks render
> their background in a solid color.
>
> Lincoln
>
> On Fri, May 29, 2009 at 3:56 PM, Angie Hinrichs <angie@...> wrote:
>
> > Mark, Do you see any error_log warnings like "ucsc_glyph: colors will
> > be out of sync ($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@...>
> > 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@...>
> > > > 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@...>
> > > > > 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@...>
> > 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 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@...
> > > > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > > > >
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > >
> > ------------------------------------------------------------------------
> > > > 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@...
> > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > >
> >
>
>
>
>
------------------------------------------------------------------------------
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@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> 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, $height);
-- so it bypasses all of the usual glyph draw() infrastructure, and
renders the entire allocated space in the main image. Using
transparency preserves the light blue lines and whatever else might be
in the background... is it not worth the trouble? Is there a better
way?
Thanks,
Angie
On Fri, 29 May 2009, Lincoln Stein wrote:
> Angie, is there any reason to call transparent()? The other tracks render
> their background in a solid color.
>
> Lincoln
>
> On Fri, May 29, 2009 at 3:56 PM, Angie Hinrichs <angie@...> wrote:
>
> > Mark, Do you see any error_log warnings like "ucsc_glyph: colors will
> > be out of sync ($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@...>
> > 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@...>
> > > > 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@...>
> > > > > 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@...>
> > 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 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@...
> > > > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > > > >
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > >
> > ------------------------------------------------------------------------
> > > > 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@...
> > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > >
> >
>
>
>
>
------------------------------------------------------------------------------
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@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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