[Insight-users] PNGwriter writes wrong scaling information

[Johnson, Hans J]

Dženan,

In other parts of ITK, the file format units are converted to mm.  While this is not strictly enforced or adhered to, in most cases converting to/from mm when writing/reading from disk seems to be the most sensible and most expected thing to do.

Hans
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Hans J. Johnson, Ph.D.
Assistant Professor, Department of Psychiatry

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From: Dženan Zukić <dzenanz at gmail.com<mailto:dzenanz at gmail.com>>
Date: Tuesday, December 11, 2012 8:42 AM
To: Bill Lorensen <bill.lorensen at gmail.com<mailto:bill.lorensen at gmail.com>>
Cc: Insight-users <insight-users at itk.org<mailto:insight-users at itk.org>>
Subject: Re: [Insight-users] PNGwriter writes wrong scaling information

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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