[Insight-users] PNGwriter writes wrong scaling information

Wed Jan 2 08:49:46 EST 2013

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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>> >>>> >> >
>> >>>> >>
>> >>>> >>
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>> >>>> >> --
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>> >>>>
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>> >>>
>> >>>
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<sCAL.png>