[Insight-users] PNGwriter writes wrong scaling information

Tue Dec 11 11:45:52 EST 2012

Can you submit as a gerrit patch?

On Tue, Dec 11, 2012 at 10:57 AM, Dženan Zukić <dzenanz at gmail.com> wrote:
> Current version of my fix is attached.
>
>
> On Tue, Dec 11, 2012 at 4:53 PM, 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 :(
>>>>> >> >> >
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>>>>> >> >
>>>>> >> >
>>>>> >>
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>>>>
>>>>
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