OpenSlide Only Recognizing Topmost Layer

[Cornwell, Carl (NIH/NLM/LHC) [C]]

A comment and a question:
1) Have you tried changing the ConvertCmd constructor argument to false in order to use ImageMagick instead of GraphicsMagick? It would seem that if the command line version produces usable output that the wrapped command should work as well.

2) Isn't the convert bundled with VIPS actually a copy of the  ImageMagick utility (with the ptif bugs fixed)?

- Carl

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Carl Cornwell
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________________________________________
From: jcupitt at gmail.com [jcupitt at gmail.com]
Sent: Wednesday, June 11, 2014 6:31 AM
To: OpenSlide users list
Subject: Re: OpenSlide Only Recognizing Topmost Layer

On 11 June 2014 09:57, Benjamin Gilbert <bgilbert at cs.cmu.edu> wrote:
> I noticed this in the im4java output:
>
>> Software: GraphicsMagick 1.3.19 2013-12-31 Q16 http://www.GraphicsMagick.org/
>
> im4java isn't using ImageMagick, it's using GraphicsMagick, which
> probably has a similar bug.  You could try reporting it to the
> GraphicsMagick developers.

This might not be a useful response, but you could also consider
another pyramid builder. VIPS (my project) is much faster than
GraphicsMagick and uses a lot less memory.

I tried on my laptop with quite a small image:

$ header summer8x3.tif
summer8x3.tif: 18008x22764 uchar, 3 bands, srgb, tiffload
$ time gm convert summer8x3.tif -define tiff:tile-geometry=256x256
-compress jpeg 'ptif:gm-pyr.tif'
real    0m50.992s
user    1m56.836s
sys    0m4.568s
peak mem: 2.4GB

My GraphicsMagick also seems to not set the sub-file type correctly.

$ time vips tiffsave summer8x3.tif vips-pyr.tif --tile --pyramid
--compression jpeg --tile-width 256 --tile-height 256
real    0m17.058s
user    0m17.348s
sys    0m1.072s
peak mem: 60MB

I tried with ImageMagick, but I think my laptop may not have enough
memory for this image

$ time convert summer8x3.tif -define tiff:tile-geometry=256x256
-compress jpeg 'ptif:im-pyr.tif'
real    7m20.224s
user    8m44.570s
sys    0m19.491s
peak mem: 4.7GB

It does set the sub-file type correctly though.

John
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