Ubuntu 14.04, Jpeg2000 and Openslide

[David Gutman]

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
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