Nanozoomer annotation coordinate system to openslide pixels

[Ahmed Bassiouni]

Hi everyone,

I am currently trying to use openslide to automatically open up nanozoomer
ndpi files and extract regions automatically. NDP annotation files (ndpa)
are used to mark ROIs. I know that annotations are not part of openslide as
of yet, but I wonder if anyone has an idea about my simple query.

The NDP annotations seems to use their own coordinate system which I can
not convert to the openslide pixel based system to extract the pictures.
(some of the point coordinates are actually negative!! weird! see example
below)

    <ndpviewstate id="1">
        <title>area 3</title>
        <details></details>
        <x>-2045952</x>
        <y>2720248</y>
        <z>0</z>
        <lens>10.000000</lens>
        <annotation type="freehand" displayname="Rectangular Area"
color="#000000">
            <measuretype>2</measuretype>
            <closed>1</closed>
            <specialtype>rectangle</specialtype>
            <pointlist>
                <point>
                    <x>-1999636</x>
                    <y>2598706</y>
                </point>
                <point>
                    <x>-1780252</x>
                    <y>2678827</y>
                </point>
                <point>
                    <x>-1831731</x>
                    <y>2819784</y>
                </point>
                <point>
                    <x>-2051115</x>
                    <y>2739663</y>
                </point>
            </pointlist>
            <specialtype>rectangle</specialtype>
        </annotation>
    </ndpviewstate>

I wonder if anyone dabbled in something like this and have an idea what
sort of scaling +/- offsetting that they use for marking ROIs like this.

There is only one github module that may be of help in this conversion, but
I failed to run the conversion code on linux and the project seems
old/abandoned.
https://github.com/Ichinaru/slideSelector

Best wishes,
Ahmed
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