[Insight-users] PNGwriter writes wrong scaling information

Thu Dec 20 17:26:11 EST 2012

I do, or can at least make one. I am on vacation until 2nd Jan, but then I
can supply one.
On Dec 20, 2012 5:06 PM, "Bill Lorensen" <bill.lorensen at gmail.com> wrote:

> I think your gerrit patch goes too far. pHYs measure pixel size/aspect
> ration. sCAL is the proper parameter, but as you pointed out, ITK is
> not writing out a correct sCAL unit type. Since ITK does not have a
> concept of unit, I think we just need to repair the output image to
> specify a valid unit type, which probably should be meters rather than
> radians.
>
> I'll modify the patch if you don't mind.
>
> Also, would you have a small png file that has a valid sCAL component?
>
> Bill
> On Tue, Dec 11, 2012 at 10:53 AM, Dženan Zukić <dzenanz at gmail.com> wrote:
> > It looks like Jim Miller introduced invalid unit usage in fix
> > 15b9450b61249261d098506d9ff878744768025a from 2003-02-19.
> >
> > PNG spec defines meters and radians as allowed units in sCAL chunk, vs
> > unknown and meters in pHYs chunk. Hence the warning I have been seeing
> with
> > OpenCV and NConvert.
> >
> >
> > On Tue, Dec 11, 2012 at 4:03 PM, Dženan Zukić <dzenanz at gmail.com> wrote:
> >>
> >> Current behavior is to ignore units, but it does not handle unit
> >> completely correctly (only handles the extension sCAL for metadata, but
> not
> >> the standard pHYs metadata).
> >>
> >> Extending current way would transform 2000 pixels/meter (pixel size 0.5
> >> mm) into spacing of 0.0005.
> >>
> >>
> >> On Tue, Dec 11, 2012 at 3:50 PM, Bradley Lowekamp <
> blowekamp at mail.nih.gov>
> >> wrote:
> >>>
> >>>
> >>> Having very small or very large spacing can have big impact on the
> >>> numerical stability of derivatives and evolving differential equations
> such
> >>> as level-sets or diffusion.
> >>>
> >>> I think the least surprising thing to the users would be to just keep
> it
> >>> the same as to avoid adverse numerical effects. Also this would not
> change
> >>> the current behavior, correct?
> >>>
> >>> Brad
> >>>
> >>> On Dec 11, 2012, at 9:42 AM, Dženan Zukić <dzenanz at gmail.com> wrote:
> >>>
> >>> PNG has three following units: meters, radians, and unknown. Currently
> >>> PNG reader ignores unit, and writes unknown units.
> >>>
> >>> I guess I Should keep writing unknown units. But when reading PNG with
> >>> meter units (eg. 2000 pixels/meter), should I transform it into pixel
> >>> spacing 0.5 (assuming customary millimeter) or into 0.0005?
> >>>
> >>>
> >>> On Tue, Dec 11, 2012 at 3:36 PM, Bill Lorensen <
> bill.lorensen at gmail.com>
> >>> wrote:
> >>>>
> >>>> No units. ITK considers units an application thing. You can add a unit
> >>>> type if the format supports it. It could help applications. For
> >>>> example, most medical images use mm's.
> >>>>
> >>>> On Tue, Dec 11, 2012 at 8:25 AM, Dženan Zukić <dzenanz at gmail.com>
> wrote:
> >>>> > Is ITK still assuming no units, or millimeters are units for pixel
> >>>> > spacing?
> >>>> >
> >>>> >
> >>>> > On Mon, Dec 10, 2012 at 5:25 PM, Bill Lorensen
> >>>> > <bill.lorensen at gmail.com>
> >>>> > wrote:
> >>>> >>
> >>>> >> If you submit a gerrit patch, I'll write or modify a test.
> >>>> >>
> >>>> >> How will we know if the fix works unless we test it? How will we
> know
> >>>> >> if someone reintroduces the bug if we don't test it?
> >>>> >>
> >>>> >>
> >>>> >> On Mon, Dec 10, 2012 at 10:41 AM, Dženan Zukić <dzenanz at gmail.com>
> >>>> >> wrote:
> >>>> >> > But this would be a bug fix, not a patch introducing new
> features.
> >>>> >> > This
> >>>> >> > should already be working, and ideally having a test.
> >>>> >> >
> >>>> >> > I know that many bugs don't get fixed, because they are not
> >>>> >> > important
> >>>> >> > enough
> >>>> >> > and there is not enough people working on ITK. However a
> >>>> >> > requirement to
> >>>> >> > write a 20-30 line test for a few lines of fixed code is a great
> >>>> >> > deterrence
> >>>> >> > for me to contribute bug fixes (such as this one).
> >>>> >> >
> >>>> >> >
> >>>> >> > On Mon, Dec 10, 2012 at 4:26 PM, Bill Lorensen
> >>>> >> > <bill.lorensen at gmail.com>
> >>>> >> > wrote:
> >>>> >> >>
> >>>> >> >> Looks like ti should be fixed. But if you submit a gerrit patch,
> >>>> >> >> make
> >>>> >> >> sure oyu also supply a test or modify an existing test.
> >>>> >> >>
> >>>> >> >> The lack of a test is why your previous gerrit patch has not
> been
> >>>> >> >> approved.
> >>>> >> >>
> >>>> >> >> Bill
> >>>> >> >>
> >>>> >> >> On Mon, Dec 10, 2012 at 8:35 AM, Dženan Zukić <
> dzenanz at gmail.com>
> >>>> >> >> wrote:
> >>>> >> >> > Hi everyone,
> >>>> >> >> >
> >>>> >> >> > I have noticed that ImageFileWriter, when writing png format,
> >>>> >> >> > writes
> >>>> >> >> > wrong
> >>>> >> >> > pixel size information. It is not completely wrong, but it is
> >>>> >> >> > not in
> >>>> >> >> > accordance with png specification.
> >>>> >> >> >
> >>>> >> >> > When reading such files with OpenCV, I get following warning:
> >>>> >> >> > libpng warning: Invalid sCAL ignored: invalid unit
> >>>> >> >> > This is not just annoying and clutter-causing, but displaying
> it
> >>>> >> >> > for
> >>>> >> >> > every
> >>>> >> >> > single image slows down my OpenCV processing.
> >>>> >> >> >
> >>>> >> >> > I used XnView to batch-edit the extracted slices and set some
> >>>> >> >> > scaling
> >>>> >> >> > which
> >>>> >> >> > adheres to the specification to get rid of this warning.
> >>>> >> >> >
> >>>> >> >> > Now the question: should I correct this bug, or submit a bug
> >>>> >> >> > report?
> >>>> >> >> > My
> >>>> >> >> > last
> >>>> >> >> > bug-fixing ended non-gloriously :(
> >>>> >> >> >
> >>>> >> >> > _____________________________________
> >>>> >> >> > Powered by www.kitware.com
> >>>> >> >> >
> >>>> >> >> > Visit other Kitware open-source projects at
> >>>> >> >> > http://www.kitware.com/opensource/opensource.html
> >>>> >> >> >
> >>>> >> >> > Kitware offers ITK Training Courses, for more information
> visit:
> >>>> >> >> > http://www.kitware.com/products/protraining.php
> >>>> >> >> >
> >>>> >> >> > Please keep messages on-topic and check the ITK FAQ at:
> >>>> >> >> > http://www.itk.org/Wiki/ITK_FAQ
> >>>> >> >> >
> >>>> >> >> > Follow this link to subscribe/unsubscribe:
> >>>> >> >> > http://www.itk.org/mailman/listinfo/insight-users
> >>>> >> >> >
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>
> >>>> >> >> --
> >>>> >> >> Unpaid intern in BillsBasement at noware dot com
> >>>> >> >
> >>>> >> >
> >>>> >>
> >>>> >>
> >>>> >>
> >>>> >> --
> >>>> >> Unpaid intern in BillsBasement at noware dot com
> >>>> >
> >>>> >
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Unpaid intern in BillsBasement at noware dot com
> >>>
> >>>
> >>> _____________________________________
> >>> Powered by www.kitware.com
> >>>
> >>> Visit other Kitware open-source projects at
> >>> http://www.kitware.com/opensource/opensource.html
> >>>
> >>> Kitware offers ITK Training Courses, for more information visit:
> >>> http://www.kitware.com/products/protraining.php
> >>>
> >>> Please keep messages on-topic and check the ITK FAQ at:
> >>> http://www.itk.org/Wiki/ITK_FAQ
> >>>
> >>> Follow this link to subscribe/unsubscribe:
> >>> http://www.itk.org/mailman/listinfo/insight-users
> >>>
> >>>
> >>
> >
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-users/attachments/20121220/03ea35a2/attachment.htm>