Ubuntu 14.04, Jpeg2000 and Openslide

[David de Mena]

Hi, David:

I have compiled OpenSlide in Unbuntu 14.4 server and working without
problems with svs files with openslide-show-properties and deepzoom.py

I have used these package:

-libglib2.0-dev
-libjpeg-dev
*-libopenjpeg-dev*
-libcario2-dev
-libpng12-dev
-libgiff5-dev
-libgdk-pixbuf2.0-dev
-libxml2-dev
-libsqlite3-dev
-valgrind

and have a ./configure result like

checking for ZLIB... yes
checking for OPENJPEG2... no
checking for OPENJPEG... no
*checking for OpenJPEG (fallback)... yes*
checking for LIBTIFF... yes
checking for GLIB2... yes
checking for CAIRO... yes
checking for LIBPNG... yes
checking for GDKPIXBUF... yes
checking for LIBXML2... yes
checking for SQLITE3... yes
checking for VALGRIND... yes

Best


David de Mena
CEO & Co-Founder
Primum Health
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2015-08-25 23:55 GMT+02:00 David Gutman <dagutman at gmail.com>:

> Has anyone had any luck with Ubuntu 14.04 and Openslide (latest from Git).
>
>
> I am getting this error:  opj_j2k_apply_nb_tile_parts_correction error
> when I try an open a file.
>
>
>
> If I run TIFFINFO on the file I get:
>
> TIFF Directory at offset 0x2df63806 (771110918)
>   Subfile Type: (0 = 0x0)
>   Image Width: 119905 Image Length: 82284 Image Depth: 1
>   Tile Width: 256 Tile Length: 256
>   Bits/Sample: 8
>   Compression Scheme: 33003 (0x80eb)
>   Photometric Interpretation: RGB color
>   Samples/Pixel: 3
>   Planar Configuration: single image plane
>   ImageDescription: Aperio Image Library v10.2.41
>
>
> So the file is JPEG2000 encoded file (compression scheme 33003)
>
> Nothing showed up on google when I typed in that string, so I wanted to
> check on the list serve.
>
> I built both openslide (3.4.1.) and openjpeg  (version 2.1.0) from source
> and the openslide make process seemed to go without any issues:
>
> checking for ZLIB... yes
> checking for OPENJPEG2... yes <<<<<<<<<<-----------------------
> checking for LIBTIFF... yes
> checking for GLIB2... yes
> checking for CAIRO... yes
> checking for LIBPNG... yes
> checking for GDKPIXBUF... yes
> checking for LIBXML2... yes
> checking for SQLITE3... yes
> checking for VALGRIND... no
>
>
>
>
> ---------------------------------------------------------------------------OpenSlideError                            Traceback (most recent call last)<ipython-input-5-d23ae8751584> in <module>()      1 import openslide      2 ----> 3 img = openslide.open_slide( curr_svs_slide_list[21])
> /home/dagutman/Envs/dsa_tools/local/lib/python2.7/site-packages/openslide/__init__.pyc in open_slide(filename)    360     object for other types of images."""    361     try:--> 362         return OpenSlide(filename)    363     except OpenSlideUnsupportedFormatError:    364         return ImageSlide(filename)
> /home/dagutman/Envs/dsa_tools/local/lib/python2.7/site-packages/openslide/__init__.pyc in __init__(self, filename)    151         """Open a whole-slide image."""    152         AbstractSlide.__init__(self)--> 153         self._osr = lowlevel.open(filename)    154     155     @classmethod
> /home/dagutman/Envs/dsa_tools/local/lib/python2.7/site-packages/openslide/lowlevel.pyc in _check_open(result, _func, _args)    139     err = get_error(slide)    140     if err is not None:--> 141         raise OpenSlideError(err)    142     return slide    143
> OpenSlideError: OpenJPEG error: opj_j2k_apply_nb_tile_parts_correction error
>
>
>
>
>
>
> --
> David A Gutman, M.D. Ph.D.
> Assistant Professor of Neurology, Psychiatry, and Biomedical Informatics
> Emory University School of Medicine
>
> _______________________________________________
> openslide-users mailing list
> openslide-users at lists.andrew.cmu.edu
> https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users
>
>
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