[Insight-users] PNGwriter writes wrong scaling information

[Bill Lorensen]

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> 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 :(
>>>> >> >> >
>>>> >> >> > _____________________________________
>>>> >> >> > Powered by www.kitware.com
>>>> >> >> >
>>>> >> >> > Visit other Kitware open-source projects at
>>>> >> >> > http://www.kitware.com/opensource/opensource.html
>>>> >> >> >
>>>> >> >> > Kitware offers ITK Training Courses, for more information visit:
>>>> >> >> > http://www.kitware.com/products/protraining.php
>>>> >> >> >
>>>> >> >> > Please keep messages on-topic and check the ITK FAQ at:
>>>> >> >> > http://www.itk.org/Wiki/ITK_FAQ
>>>> >> >> >
>>>> >> >> > Follow this link to subscribe/unsubscribe:
>>>> >> >> > http://www.itk.org/mailman/listinfo/insight-users
>>>> >> >> >
>>>> >> >>
>>>> >> >>
>>>> >> >>
>>>> >> >> --
>>>> >> >> Unpaid intern in BillsBasement at noware dot com
>>>> >> >
>>>> >> >
>>>> >>
>>>> >>
>>>> >>
>>>> >> --
>>>> >> Unpaid intern in BillsBasement at noware dot com
>>>> >
>>>> >
>>>>
>>>>
>>>>
>>>> --
>>>> Unpaid intern in BillsBasement at noware dot com
>>>
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://www.itk.org/mailman/listinfo/insight-users
>>>
>>>
>>
>



-- 
Unpaid intern in BillsBasement at noware dot com