<div dir="ltr">Hi, David:<div><br></div><div>I have compiled OpenSlide in Unbuntu 14.4 server and working without problems with svs files with openslide-show-properties and deepzoom.py</div><div><br></div><div>I have used these package:</div><div><br></div><div><div>-libglib2.0-dev</div><div>-libjpeg-dev</div><div><b>-libopenjpeg-dev</b></div><div>-libcario2-dev</div><div>-libpng12-dev</div><div>-libgiff5-dev</div><div>-libgdk-pixbuf2.0-dev</div><div>-libxml2-dev</div><div>-libsqlite3-dev</div><div>-valgrind</div></div><div><br></div><div>and have a ./configure result like </div><div><br></div><div><div>checking for ZLIB... yes</div><div>checking for OPENJPEG2... no</div><div>checking for OPENJPEG... no</div><div><b>checking for OpenJPEG (fallback)... yes</b></div><div>checking for LIBTIFF... yes</div><div>checking for GLIB2... yes</div><div>checking for CAIRO... yes</div><div>checking for LIBPNG... yes</div><div>checking for GDKPIXBUF... yes</div><div>checking for LIBXML2... yes</div><div>checking for SQLITE3... yes</div><div>checking for VALGRIND... yes</div></div><div><br></div><div>Best</div><div><br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature">David de Mena<br>CEO & Co-Founder<br>Primum Health<br><a href="http://www.primum.es" target="_blank">www.primum.es</a><<a href="http://www.primum.es/" target="_blank">http://www.primum.es/</a>><br>Presentación<<a href="http://link.primum.es/P_es" target="_blank">http://link.primum.es/P_es</a>> y Brochure<<a href="http://link.primum.es/B_es" target="_blank">http://link.primum.es/B_es</a>><br><br>[Síguenos en Twitter]<<a href="https://twitter.com/Primum_es" target="_blank">https://twitter.com/Primum_es</a>><br>[Síguenos en facebook]<<a href="https://www.facebook.com/PrimumHealthIt" target="_blank">https://www.facebook.com/PrimumHealthIt</a>><br>[Síguenos en YouTube]<<a href="http://www.youtube.com/primumhealth" target="_blank">http://www.youtube.com/primumhealth</a>><br><br><br></div></div>
<br><div class="gmail_quote">2015-08-25 23:55 GMT+02:00 David Gutman <span dir="ltr"><<a href="mailto:dagutman@gmail.com" target="_blank">dagutman@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Has anyone had any luck with Ubuntu 14.04 and Openslide (latest from Git).<br></div><div><br></div><div><br></div><div>I am getting this error: opj_j2k_apply_nb_tile_parts_correction error when I try an open a file.<br></div><div><br></div><div><br></div><div><br></div><div>If I run TIFFINFO on the file I get: </div><div><br></div><div>TIFF Directory at offset 0x2df63806 (771110918)</div><div> Subfile Type: (0 = 0x0)</div><div> Image Width: 119905 Image Length: 82284 Image Depth: 1</div><div> Tile Width: 256 Tile Length: 256</div><div> Bits/Sample: 8</div><div> Compression Scheme: 33003 (0x80eb)</div><div> Photometric Interpretation: RGB color</div><div> Samples/Pixel: 3</div><div> Planar Configuration: single image plane</div><div> ImageDescription: Aperio Image Library v10.2.41</div><div><br></div><div><br></div><div>So the file is JPEG2000 encoded file (compression scheme 33003)</div><div><br></div><div>Nothing showed up on google when I typed in that string, so I wanted to check on the list serve.<br></div><br>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:<br><br>checking for ZLIB... yes<br>checking for OPENJPEG2... yes <<<<<<<<<<-----------------------<br>checking for LIBTIFF... yes<br>checking for GLIB2... yes<br>checking for CAIRO... yes<br>checking for LIBPNG... yes<br>checking for GDKPIXBUF... yes<br>checking for LIBXML2... yes<br>checking for SQLITE3... yes<br>checking for VALGRIND... no<br><br><div><font color="#c4a000"><span style="white-space:pre-wrap"><br></span></font></div><div><font color="#c4a000"><span style="white-space:pre-wrap"><br></span></font><br><div style="min-width:14ex;padding:0px 0.4em;margin:0px;font-family:monospace;text-align:right;line-height:1.21429em;color:rgb(0,0,0);font-size:14px"></div><div style="padding:0.4em;max-width:calc(100% - 14ex);color:rgb(0,0,0);line-height:1.21429em;font-family:'Helvetica Neue',Helvetica,Arial,sans-serif;font-size:14px"><pre style="overflow:auto;font-size:inherit;padding:0px;margin-top:0px;margin-bottom:0px;line-height:inherit;word-wrap:break-word;border:0px;border-radius:0px;white-space:pre-wrap;vertical-align:baseline;background-color:transparent"><span style="color:rgb(139,0,0)">---------------------------------------------------------------------------</span>
<span style="color:rgb(139,0,0)">OpenSlideError</span> Traceback (most recent call last)
<span style="color:rgb(0,100,0)"><ipython-input-5-d23ae8751584></span> in <span style="color:rgb(70,130,180)"><module><span style="color:rgb(0,0,139)">()</span>
<span style="color:rgb(0,100,0)"> 1</span> <span style="color:rgb(0,100,0)">import</span> openslide<span style="color:rgb(196,160,0)"></span>
<span style="color:rgb(0,100,0)"> 2</span> <span style="color:rgb(196,160,0)"></span>
<span style="color:rgb(0,100,0)">----> 3<span style="color:rgb(196,160,0)"> </span>img <span style="color:rgb(196,160,0)">=</span> openslide<span style="color:rgb(196,160,0)">.</span>open_slide<span style="color:rgb(196,160,0)">(</span> curr_svs_slide_list<span style="color:rgb(196,160,0)">[</span><span style="color:rgb(70,130,180)">21</span><span style="color:rgb(196,160,0)">]</span><span style="color:rgb(196,160,0)">)</span><span style="color:rgb(196,160,0)"></span>
<span>/home/dagutman/Envs/dsa_tools/local/lib/python2.7/site-packages/openslide/__init__.pyc</span> in <span style="color:rgb(70,130,180)">open_slide<span style="color:rgb(0,0,139)">(filename)</span>
<span style="color:rgb(0,100,0)"> 360</span> object for other types of images."""
<span style="color:rgb(0,100,0)"> 361</span> <span style="color:rgb(0,100,0)">try</span><span style="color:rgb(196,160,0)">:</span><span style="color:rgb(196,160,0)"></span>
<span style="color:rgb(0,100,0)">--> 362<span style="color:rgb(196,160,0)"> <span style="color:rgb(0,100,0)">return</span> OpenSlide<span>(</span>filename<span>)</span><span></span>
<span style="color:rgb(0,100,0)"> 363</span> <span style="color:rgb(0,100,0)">except</span> OpenSlideUnsupportedFormatError<span>:</span><span></span>
<span style="color:rgb(0,100,0)"> 364</span> <span style="color:rgb(0,100,0)">return</span> ImageSlide<span>(</span>filename<span>)</span><span></span>
<span style="color:rgb(0,100,0)">/home/dagutman/Envs/dsa_tools/local/lib/python2.7/site-packages/openslide/__init__.pyc</span> in <span style="color:rgb(70,130,180)">__init__<span style="color:rgb(0,0,139)">(self, filename)</span>
<span style="color:rgb(0,100,0)"> 151</span> <span style="color:rgb(0,0,139)">"""Open a whole-slide image."""</span><span style="color:rgb(196,160,0)"></span>
<span style="color:rgb(0,100,0)"> 152</span> AbstractSlide<span style="color:rgb(196,160,0)">.</span>__init__<span style="color:rgb(196,160,0)">(</span>self<span style="color:rgb(196,160,0)">)</span><span style="color:rgb(196,160,0)"></span>
<span style="color:rgb(0,100,0)">--> 153<span style="color:rgb(196,160,0)"> </span>self<span style="color:rgb(196,160,0)">.</span>_osr <span style="color:rgb(196,160,0)">=</span> lowlevel<span style="color:rgb(196,160,0)">.</span>open<span style="color:rgb(196,160,0)">(</span>filename<span style="color:rgb(196,160,0)">)</span><span style="color:rgb(196,160,0)"></span>
<span> 154</span> <span style="color:rgb(196,160,0)"></span>
<span> 155</span> <span style="color:rgb(196,160,0)">@</span>classmethod<span style="color:rgb(196,160,0)"></span>
<span>/home/dagutman/Envs/dsa_tools/local/lib/python2.7/site-packages/openslide/lowlevel.pyc</span> in <span style="color:rgb(70,130,180)">_check_open<span style="color:rgb(0,0,139)">(result, _func, _args)</span>
<span style="color:rgb(0,100,0)"> 139</span> err <span style="color:rgb(196,160,0)">=</span> get_error<span style="color:rgb(196,160,0)">(</span>slide<span style="color:rgb(196,160,0)">)</span><span style="color:rgb(196,160,0)"></span>
<span style="color:rgb(0,100,0)"> 140</span> <span style="color:rgb(0,100,0)">if</span> err <span style="color:rgb(0,100,0)">is</span> <span style="color:rgb(0,100,0)">not</span> None<span style="color:rgb(196,160,0)">:</span><span style="color:rgb(196,160,0)"></span>
<span style="color:rgb(0,100,0)">--> 141<span style="color:rgb(196,160,0)"> <span style="color:rgb(0,100,0)">raise</span> OpenSlideError<span>(</span>err<span>)</span><span></span>
<span style="color:rgb(0,100,0)"> 142</span> <span style="color:rgb(0,100,0)">return</span> slide<span></span>
<span style="color:rgb(0,100,0)"> 143</span> <span></span>
<span style="color:rgb(139,0,0)">OpenSlideError</span>: OpenJPEG error: opj_j2k_apply_nb_tile_parts_correction error
</span></span></span></span></span></span></span></span></span></span></pre><div><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(196,160,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(196,160,0)"><br></span></span></span></span></span></span></span></span></span></span></div></div><br><br><br><br>--<br>David A Gutman, M.D. Ph.D.<br>Assistant Professor of Neurology, Psychiatry, and Biomedical Informatics<br>Emory University School of Medicine
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<br></blockquote></div><br></div>