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https://issues.apache.org/jira/browse/PDFBOX-1960?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13922577#comment-13922577
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Maruan Sahyoun commented on PDFBOX-1960:
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Although the differences might be confusing Matrix and it’s layout is defined 
in the PDF spec. So that’s why its behaving as is. Of course there are 
differences to AffineTransform as it’s dealing with a different definition and 
layout of a matrix. So conceptually being the same the do differ.

The only way I see that improvement request to being resolved is adding some 
more documentation - WDYT? Other ideas? 

> Matrix and AffineTransform have confusing differences
> -----------------------------------------------------
>
>                 Key: PDFBOX-1960
>                 URL: https://issues.apache.org/jira/browse/PDFBOX-1960
>             Project: PDFBox
>          Issue Type: Improvement
>    Affects Versions: 2.0.0
>            Reporter: John Hewson
>            Assignee: Maruan Sahyoun
>            Priority: Minor
>
> I've been driven insane recently by trying to get pattern fills to render 
> correctly. Patterns have their own matrix which is concatenated to the CTM 
> and no matter how I applied the transformation, the results were wrong.
> It turns out that org.apache.pdfbox.util.Matrix is not behaving as expected, 
> here's an example from a pattern I'm working on. I performed the same 
> concatenation (i.e. multiplication) using our Matrix and Java's 
> AffineTransform, the results are as follows:
> Java AffineTransform:
> [[2.0, 0.0, 1.251E-12], [0.0, 2.0, 1684.0]] *
> [[0.6, 0.0, 302.6], [0.0, 0.6, 1091.38]] =
> [[1.2, 0.0, 605.2000000000013], [0.0, 1.2, 3866.76]]
> PDFBox Matrix:
> [[2.0,0.0,0.0][0.0,2.0,0.0][1.251E-12,1684.0,1.0]] *
> [[0.6,0.0,0.0][0.0,0.6,0.0][302.6,1091.38,1.0]] =
> [[1.2,0.0,0.0][0.0,1.2,0.0][302.6,2101.78,1.0]]
> I suggest that we remove Matrix and replace it with AffineTransform.



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