[ITK] [ITK-dev] Probelms with recent "Image spacing must be positive" change...

Fri Jul 21 13:31:53 EDT 2017

Sean,

The other patch related to this change is the following:

https://github.com/InsightSoftwareConsortium/ITK/commit/d447f0452bb5ea92a555e630d05b57da535bd3a9
ENH: Explicitly warn and deprecate negative pixel spacing.
The DICOM standard explicitly disallows negative pixel spacing:
http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_10.7.html#sect_10.7.1.3

Additionally, it is fundamentally unnatural to have negative space or
"size" of an object. The negative is a directional information which
should be contained in the direction cosine matrix not the spacing
attribute.

Change-Id: I1519faee14f48d2eecc08e100562f820eb6aa6ef

Are you proposing a flag in the  ImageFileReader class? What bout the Series reader? Will it be placed in the MetaData dictionary?

> What do you think about adding an API so that it can be known if/which axes were flipped?
The wording is going to tricky. Some file formats native coordinates are LPS ( ITK ) while others are RAS, so there may be some “flipping” already done during reading in ImageIO classes.

As the ImageFileReader is doing the conversion and not the ImageIO, would it suffices to just query ImageIO::GetSpacing to see if it’s changed?

Brad

On 7/21/17, 12:35 PM, "Sean McBride" <sean at rogue-research.com> wrote:

    On Fri, 2 Jun 2017 16:18:37 -0400, Sean McBride said:

    >7501479a970694b0dd4a8c4bbf7cbcc033fe059c is the first bad commit
    >commit 7501479a970694b0dd4a8c4bbf7cbcc033fe059c
    >Author: Francois Budin <francois.budin at gmail.com>
    >Date:   Mon Oct 31 17:04:05 2016 -0400
    >
    >    ENH: Image spacing must be positive
    >    
    >    Image spacing must have values greater than 0. Negative
    >    values could create issues with filters that assume that they
    >    are positive.
    >    When an image is loaded, if its spacing is negative, its absolute
    >    value is kept, and the image direction along each axis with a
    >    negative spacing is flipped.
    >    
    >    Change-Id: Id81d61b7fd3f60df2b38e30e540664dba6264996
    >
    >Which is here:
    ><http://review.source.kitware.com/#/c/21685/>
    >
    >Looks like this shipped in 4.11 (we are using 4.10.1).
    >
    >Our test case is an Analyze 7.5 file with negative spacing.  I'll dig
    >into it next week...

    François, Matt,

    So this change is causing us backwards-compatibility problems.

    What do you think about adding an API so that it can be known if/which axes were flipped?  As it is now, the flipping newly performed by ITK cannot be detected.  If such a change is acceptable, I can make a patch...

    (Our app used to warn users that files with negative spacing are problematic, but now we have no means to generate this warning, unless I'm missing something.)

    Thanks,

    Sean

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