[Insight-users] PNGwriter writes wrong scaling information

Wed Jan 2 17:12:25 EST 2013

Jim,

Let's look at this next week in SLC. I spent some time trying to
understand the difference between pHYs and sCAL. It should not take
much time to get a working patch based on Dženan patch.

Bill

On Wed, Jan 2, 2013 at 8:59 AM, Dženan Zukić <dzenanz at gmail.com> wrote:
> 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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>> >> >>>> >> >>
>> >> >>>> >> >>
>> >> >>>> >> >>
>> >> >>>> >> >> --
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>> >> >>>> >> >
>> >> >>>> >>
>> >> >>>> >>
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>> >> >>>
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>>
>> <sCAL.png>
>>
>

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