<p>I do, or can at least make one. I am on vacation until 2nd Jan, but then I can supply one.</p>
<div class="gmail_quote">On Dec 20, 2012 5:06 PM, "Bill Lorensen" <<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I think your gerrit patch goes too far. pHYs measure pixel size/aspect<br>
ration. sCAL is the proper parameter, but as you pointed out, ITK is<br>
not writing out a correct sCAL unit type. Since ITK does not have a<br>
concept of unit, I think we just need to repair the output image to<br>
specify a valid unit type, which probably should be meters rather than<br>
radians.<br>
<br>
I'll modify the patch if you don't mind.<br>
<br>
Also, would you have a small png file that has a valid sCAL component?<br>
<br>
Bill<br>
On Tue, Dec 11, 2012 at 10:53 AM, Dženan Zukić <<a href="mailto:dzenanz@gmail.com">dzenanz@gmail.com</a>> wrote:<br>
> It looks like Jim Miller introduced invalid unit usage in fix<br>
> 15b9450b61249261d098506d9ff878744768025a from 2003-02-19.<br>
><br>
> PNG spec defines meters and radians as allowed units in sCAL chunk, vs<br>
> unknown and meters in pHYs chunk. Hence the warning I have been seeing with<br>
> OpenCV and NConvert.<br>
><br>
><br>
> On Tue, Dec 11, 2012 at 4:03 PM, Dženan Zukić <<a href="mailto:dzenanz@gmail.com">dzenanz@gmail.com</a>> wrote:<br>
>><br>
>> Current behavior is to ignore units, but it does not handle unit<br>
>> completely correctly (only handles the extension sCAL for metadata, but not<br>
>> the standard pHYs metadata).<br>
>><br>
>> Extending current way would transform 2000 pixels/meter (pixel size 0.5<br>
>> mm) into spacing of 0.0005.<br>
>><br>
>><br>
>> On Tue, Dec 11, 2012 at 3:50 PM, Bradley Lowekamp <<a href="mailto:blowekamp@mail.nih.gov">blowekamp@mail.nih.gov</a>><br>
>> wrote:<br>
>>><br>
>>><br>
>>> Having very small or very large spacing can have big impact on the<br>
>>> numerical stability of derivatives and evolving differential equations such<br>
>>> as level-sets or diffusion.<br>
>>><br>
>>> I think the least surprising thing to the users would be to just keep it<br>
>>> the same as to avoid adverse numerical effects. Also this would not change<br>
>>> the current behavior, correct?<br>
>>><br>
>>> Brad<br>
>>><br>
>>> On Dec 11, 2012, at 9:42 AM, Dženan Zukić <<a href="mailto:dzenanz@gmail.com">dzenanz@gmail.com</a>> wrote:<br>
>>><br>
>>> PNG has three following units: meters, radians, and unknown. Currently<br>
>>> PNG reader ignores unit, and writes unknown units.<br>
>>><br>
>>> I guess I Should keep writing unknown units. But when reading PNG with<br>
>>> meter units (eg. 2000 pixels/meter), should I transform it into pixel<br>
>>> spacing 0.5 (assuming customary millimeter) or into 0.0005?<br>
>>><br>
>>><br>
>>> On Tue, Dec 11, 2012 at 3:36 PM, Bill Lorensen <<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>><br>
>>> wrote:<br>
>>>><br>
>>>> No units. ITK considers units an application thing. You can add a unit<br>
>>>> type if the format supports it. It could help applications. For<br>
>>>> example, most medical images use mm's.<br>
>>>><br>
>>>> On Tue, Dec 11, 2012 at 8:25 AM, Dženan Zukić <<a href="mailto:dzenanz@gmail.com">dzenanz@gmail.com</a>> wrote:<br>
>>>> > Is ITK still assuming no units, or millimeters are units for pixel<br>
>>>> > spacing?<br>
>>>> ><br>
>>>> ><br>
>>>> > On Mon, Dec 10, 2012 at 5:25 PM, Bill Lorensen<br>
>>>> > <<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>><br>
>>>> > wrote:<br>
>>>> >><br>
>>>> >> If you submit a gerrit patch, I'll write or modify a test.<br>
>>>> >><br>
>>>> >> How will we know if the fix works unless we test it? How will we know<br>
>>>> >> if someone reintroduces the bug if we don't test it?<br>
>>>> >><br>
>>>> >><br>
>>>> >> On Mon, Dec 10, 2012 at 10:41 AM, Dženan Zukić <<a href="mailto:dzenanz@gmail.com">dzenanz@gmail.com</a>><br>
>>>> >> wrote:<br>
>>>> >> > But this would be a bug fix, not a patch introducing new features.<br>
>>>> >> > This<br>
>>>> >> > should already be working, and ideally having a test.<br>
>>>> >> ><br>
>>>> >> > I know that many bugs don't get fixed, because they are not<br>
>>>> >> > important<br>
>>>> >> > enough<br>
>>>> >> > and there is not enough people working on ITK. However a<br>
>>>> >> > requirement to<br>
>>>> >> > write a 20-30 line test for a few lines of fixed code is a great<br>
>>>> >> > deterrence<br>
>>>> >> > for me to contribute bug fixes (such as this one).<br>
>>>> >> ><br>
>>>> >> ><br>
>>>> >> > On Mon, Dec 10, 2012 at 4:26 PM, Bill Lorensen<br>
>>>> >> > <<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>><br>
>>>> >> > wrote:<br>
>>>> >> >><br>
>>>> >> >> Looks like ti should be fixed. But if you submit a gerrit patch,<br>
>>>> >> >> make<br>
>>>> >> >> sure oyu also supply a test or modify an existing test.<br>
>>>> >> >><br>
>>>> >> >> The lack of a test is why your previous gerrit patch has not been<br>
>>>> >> >> approved.<br>
>>>> >> >><br>
>>>> >> >> Bill<br>
>>>> >> >><br>
>>>> >> >> On Mon, Dec 10, 2012 at 8:35 AM, Dženan Zukić <<a href="mailto:dzenanz@gmail.com">dzenanz@gmail.com</a>><br>
>>>> >> >> wrote:<br>
>>>> >> >> > Hi everyone,<br>
>>>> >> >> ><br>
>>>> >> >> > I have noticed that ImageFileWriter, when writing png format,<br>
>>>> >> >> > writes<br>
>>>> >> >> > wrong<br>
>>>> >> >> > pixel size information. It is not completely wrong, but it is<br>
>>>> >> >> > not in<br>
>>>> >> >> > accordance with png specification.<br>
>>>> >> >> ><br>
>>>> >> >> > When reading such files with OpenCV, I get following warning:<br>
>>>> >> >> > libpng warning: Invalid sCAL ignored: invalid unit<br>
>>>> >> >> > This is not just annoying and clutter-causing, but displaying it<br>
>>>> >> >> > for<br>
>>>> >> >> > every<br>
>>>> >> >> > single image slows down my OpenCV processing.<br>
>>>> >> >> ><br>
>>>> >> >> > I used XnView to batch-edit the extracted slices and set some<br>
>>>> >> >> > scaling<br>
>>>> >> >> > which<br>
>>>> >> >> > adheres to the specification to get rid of this warning.<br>
>>>> >> >> ><br>
>>>> >> >> > Now the question: should I correct this bug, or submit a bug<br>
>>>> >> >> > report?<br>
>>>> >> >> > My<br>
>>>> >> >> > last<br>
>>>> >> >> > bug-fixing ended non-gloriously :(<br>
>>>> >> >> ><br>
>>>> >> >> > _____________________________________<br>
>>>> >> >> > Powered by <a href="http://www.kitware.com" target="_blank">www.kitware.com</a><br>
>>>> >> >> ><br>
>>>> >> >> > Visit other Kitware open-source projects at<br>
>>>> >> >> > <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
>>>> >> >> ><br>
>>>> >> >> > Kitware offers ITK Training Courses, for more information visit:<br>
>>>> >> >> > <a href="http://www.kitware.com/products/protraining.php" target="_blank">http://www.kitware.com/products/protraining.php</a><br>
>>>> >> >> ><br>
>>>> >> >> > Please keep messages on-topic and check the ITK FAQ at:<br>
>>>> >> >> > <a href="http://www.itk.org/Wiki/ITK_FAQ" target="_blank">http://www.itk.org/Wiki/ITK_FAQ</a><br>
>>>> >> >> ><br>
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>>>> >> >> ><br>
>>>> >> >><br>
>>>> >> >><br>
>>>> >> >><br>
>>>> >> >> --<br>
>>>> >> >> Unpaid intern in BillsBasement at noware dot com<br>
>>>> >> ><br>
>>>> >> ><br>
>>>> >><br>
>>>> >><br>
>>>> >><br>
>>>> >> --<br>
>>>> >> Unpaid intern in BillsBasement at noware dot com<br>
>>>> ><br>
>>>> ><br>
>>>><br>
>>>><br>
>>>><br>
>>>> --<br>
>>>> Unpaid intern in BillsBasement at noware dot com<br>
>>><br>
>>><br>
>>> _____________________________________<br>
>>> Powered by <a href="http://www.kitware.com" target="_blank">www.kitware.com</a><br>
>>><br>
>>> Visit other Kitware open-source projects at<br>
>>> <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
>>><br>
>>> Kitware offers ITK Training Courses, for more information visit:<br>
>>> <a href="http://www.kitware.com/products/protraining.php" target="_blank">http://www.kitware.com/products/protraining.php</a><br>
>>><br>
>>> Please keep messages on-topic and check the ITK FAQ at:<br>
>>> <a href="http://www.itk.org/Wiki/ITK_FAQ" target="_blank">http://www.itk.org/Wiki/ITK_FAQ</a><br>
>>><br>
>>> Follow this link to subscribe/unsubscribe:<br>
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>>><br>
>>><br>
>><br>
><br>
<br>
<br>
<br>
--<br>
Unpaid intern in BillsBasement at noware dot com<br>
</blockquote></div>