[Insight-users] PNGwriter writes wrong scaling information

[Dženan Zukić]

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 :(
>> >> >> >
>> >> >> > _____________________________________
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>> >> >
>> >> >
>> >>
>> >>
>> >>
>> >> --
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>>
>>
>>
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>>
>
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