[Insight-users] PNGwriter writes wrong scaling information

[Dženan Zukić]

No. After the first image got stuck due to oversize, I cropped it, but that
was still too large so I cropped it some more. The spacing (0.5 mm) should
be correct for the last (smallest) one.


On Wed, Jan 2, 2013 at 2:49 PM, Miller, James V (GE Global Research) <
millerjv at ge.com> wrote:

> I am assuming these are three images that were resampled to different
> resolutions with the sCAL information adjusted so the pixel sizes change.
>  Is this correct?
>
>
> Jim Miller
> Senior Scientist
> GE Research
> Interventional and Therapy
>
> GE imagination at work
>
>
>
> On Jan 2, 2013, at 7:24 AM, Dženan Zukić wrote:
>
> PNG image with sCAL chunk attached.
>
>
> On Fri, Dec 21, 2012 at 12:57 AM, Bill Lorensen <bill.lorensen at gmail.com
> <mailto:bill.lorensen at gmail.com>> wrote:
> That will be great.
>
> Happy New Tear,
>
> Bill
>
> On Thu, Dec 20, 2012 at 5:26 PM, Dženan Zukić <dzenanz at gmail.com<mailto:
> dzenanz at gmail.com>> wrote:
> > 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
> <mailto: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
> <mailto: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
> <mailto: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<mailto: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
> <mailto: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<mailto: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
> <mailto: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<mailto: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<mailto: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<mailto: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<mailto: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 :(
> >> >>>> >> >> >
> >> >>>> >> >> > _____________________________________
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> >> >>>> >> >> >
> >> >>>> >> >> > Visit other Kitware open-source projects at
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> >> >>>> >> >> >
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> >> >>>> >> >> >
> >> >>>> >> >> > Please keep messages on-topic and check the ITK FAQ at:
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> >> >>>> >> >> >
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> >> >>>> >> >> >
> >> >>>> >> >>
> >> >>>> >> >>
> >> >>>> >> >>
> >> >>>> >> >> --
> >> >>>> >> >> Unpaid intern in BillsBasement at noware dot com
> >> >>>> >> >
> >> >>>> >> >
> >> >>>> >>
> >> >>>> >>
> >> >>>> >>
> >> >>>> >> --
> >> >>>> >> Unpaid intern in BillsBasement at noware dot com
> >> >>>> >
> >> >>>> >
> >> >>>>
> >> >>>>
> >> >>>>
> >> >>>> --
> >> >>>> Unpaid intern in BillsBasement at noware dot com
> >> >>>
> >> >>>
> >> >>> _____________________________________
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> >> >>>
> >> >>> Visit other Kitware open-source projects at
> >> >>> http://www.kitware.com/opensource/opensource.html
> >> >>>
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> >> >>
> >> >
> >>
> >>
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>
> --
> Unpaid intern in BillsBasement at noware dot com
>
> <sCAL.png>
>
>
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