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Apologies I meant this thread:<div><a href="http://www.openmicroscopy.org/community/viewtopic.php?f=6&t=694" style="font-size: 10pt; ">http://www.openmicroscopy.org/community/viewtopic.php?f=6&t=694</a><span style="font-size: 10pt; "> </span></div><div><br></div><div>J.</div><div><br><div><div id="SkyDrivePlaceholder"></div><hr id="stopSpelling">From: jeromeavondo@msn.com<br>To: will@lifesci.dundee.ac.uk<br>Date: Thu, 22 Mar 2012 15:18:54 +0000<br>CC: ome-devel@lists.openmicroscopy.org.uk<br>Subject: Re: [ome-devel] RenderingEngine: setting channel colours<br><br>
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<div>Hi Will,</div><div><br></div><div>Thanks for the info...</div><div><span style="font-size:10pt">I saw that thread, but kept getting an "omero::OptimisticLockException" when trying that approach...</span></div><div><br></div><div>So I was following this thread, since it helped greatly to allow me to upload data...</div><div><a href="https://www.openmicroscopy.org/community/viewtopic.php?f=6&t=768" style="font-size:10pt" target="_blank">https://www.openmicroscopy.org/community/viewtopic.php?f=6&t=768</a></div><div><br></div><div>Just to make sure I understand the difference between setting channel colours <span style="font-size:10pt">via the RenderingEngine vs Channel objects....</span></div><div>The RenderingEngine is a per user setting, whilst doing it on the Channel object will make it the default for all users?</div><div><br></div><div>Using your code, I changed mine to the following, however I still get the <span style="font-size:10pt">"omero::OptimisticLockException"... </span></div><div><br></div><div><div> std::string query = "select p from Pixels p join fetch p.channels as c join fetch c.logicalChannel as lc where p.id=:pid";</div><div> omero::sys::ParametersIPtr params = new omero::sys::ParametersI();</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>params->add("pid", omero::rtypes::rlong(pixid));</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>omero::api::IObjectList resultobjs = queryService->findAllByQuery(query, params);</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>if(resultobjs.empty()) </div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>{</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>printf("ERROR: Could not find pixels object\n");</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>return;</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>}</div><div><br></div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>pixels = omero::model::PixelsPtr::dynamicCast(resultobjs[0]);</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>for(int c=0; c<csize; c++)</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>{</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>omero::model::ChannelPtr chan = pixels->getChannel(c);</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>omero::model::IObjectPtr obj = queryService->get("Channel", chan->getId()->getValue());</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>chan = omero::model::ChannelPtr::dynamicCast(obj);<span class="ecxApple-tab-span" style="white-space:pre"> </span></div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>chan->setRed(omero::rtypes::rint(0));</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>chan->setGreen(omero::rtypes::rint(255));</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>chan->setBlue(omero::rtypes::rint(0));</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>chan->setAlpha(omero::rtypes::rint(255));</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>gateway->saveObject(chan);</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>}</div><div> sf->getDeleteService()->deleteSettings(imageID);</div></div><div><br></div><div>Any idea what I'm doing wrong?</div><div>Thanks!</div><div><br></div><div>J.</div><div><br></div><div>Subject: Re: [ome-devel] RenderingEngine: setting channel colours<br>From: will@lifesci.dundee.ac.uk<br>Date: Thu, 22 Mar 2012 13:03:52 +0000<br>CC: jeromeavondo@msn.com; ome-devel@lists.openmicroscopy.org.uk<br>To: will@lifesci.dundee.ac.uk<br><br>
<div>Hi Jerome,</div><div><br></div><div>You can also see this discussed on our forums (Python again I'm afraid)</div><div><br></div><a href="https://www.openmicroscopy.org/community/viewtopic.php?f=6&t=768" target="_blank">https://www.openmicroscopy.org/community/viewtopic.php?f=6&t=768</a><div><br></div><div>which was the first hit when I Googled:</div><div>omero forum setting channel colours</div><div><br></div><div>Cheers,</div><div><br></div><div> Will. </div><div><br></div><div><br><div><br><div><div>On 22 Mar 2012, at 13:00, Will Moore wrote:</div><br class="ecxApple-interchange-newline"><blockquote><div style="word-wrap:break-word">Hi Jerome,<div><br></div><div>The best way of doing this is to set the colours on the Channels themselves, then reset the default rendering settings.</div><div>This means that whenever any user resets their rendering settings on the image, they will default to the 'correct' colours. </div><div><br></div><div>Here's some (pseudo code) of what I'm doing in Python - Hopefully you can work out the C++</div><div>Not sure if you'll have to reload as I'm doing. Try it and see.</div><div><br></div><div>You can get channels via pixels,</div><div>EITHER via the rendering engine (once you've set Ids etc)...</div><div><br></div><div>pixels = re.getPixels()</div><div><br></div><div><br></div><div>OR via the query service...</div><div><br></div><div><div>pid = image.getPrimaryPixels().getId().getValue()</div><div>params = omero.sys.Parameters()</div><div>params.map = {"pid": rlong(pid)}</div><div>query = "select p from Pixels p join fetch p.channels as c join fetch c.logicalChannel as lc where p.id=:pid"</div><div>pixels = session.getQueryService().findByQuery(query, params)</div></div><div><br></div><div>for c in pixels.iterateChannels():</div><div><span class="ecxApple-tab-span" style="white-space:pre"> # </span>??? <span class="ecxApple-tab-span" style="white-space:pre">need to reload channels to avoid optimistic lock on update</span> ??? <span class="ecxApple-tab-span" style="white-space:pre">
</span>c<span class="ecxApple-tab-span" style="white-space:pre"> = conn.getQueryService().get("Channel", c.id</span>.val<span class="ecxApple-tab-span" style="white-space:pre">) </span># could try to skip this step</div><div><br></div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>c.red = omero.rtypes.rint(r)</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>c.green = omero.rtypes.rint(g)</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>c.blue = omero.rtypes.rint(b)</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>c.alpha = omero.rtypes.rint(255)</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>session.getUpdateService().saveObject(c)</div><div><br></div><div><br></div><div>Than reset </div><div>session.getDeleteService().deleteSettings(imageId)</div><div><br></div><div><div>If this doesn't work, maybe also try:</div><div>renderingEngine.resetDefaults()</div></div><div><br></div><div><br></div><div> Let us know how you get on,</div><div><br></div><div><br></div><div> Will</div><div><br></div><div><br></div><div><br></div><div><div><div>On 22 Mar 2012, at 12:11, Jerome Avondo wrote:</div><br class="ecxApple-interchange-newline"><blockquote><div class="ecxhmmessage" style="font-size:10pt;font-family:Tahoma"><div dir="ltr">Hi,<div><br></div><div>I am trying to set the rendering colours for an image I upload to the server via the C++ API...</div><div>The image upload is all good, but I am a little confused with setting the rendering options...</div><div><span style="font-size:10pt">I am uploading a 3 channel image, and I set the render settings as follows:</span></div><div><br></div><div><span class="ecxApple-tab-span" style="font-size:10pt;white-space:pre"> </span><span style="font-size:10pt">for(int c=0; c<csize; c++)</span></div><div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>{</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>if(c==0)</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>{</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>renderingEngine->setChannelWindow(c, float(0), float(255));</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>renderingEngine->setRGBA(c, 255, 0, 0, 255);</div><div><span class="ecxApple-tab-span" style="font-size:10pt;white-space:pre"> </span><span style="font-size:10pt">}</span></div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>if(c==1)</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>{</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>renderingEngine->setChannelWindow(c, float(0), float(255));</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>renderingEngine->setRGBA(c, 0, 255, 0, 255);</div><div><span class="ecxApple-tab-span" style="font-size:10pt;white-space:pre"> </span><span style="font-size:10pt">}</span></div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>if(c==2)</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>{</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>renderingEngine->setChannelWindow(c, float(0), float(255));</div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>renderingEngine->setRGBA(c, 0, 0, 255, 255);</div><div><span class="ecxApple-tab-span" style="font-size:10pt;white-space:pre"> </span><span style="font-size:10pt">}</span></div><div><span class="ecxApple-tab-span" style="font-size:10pt;white-space:pre"> </span><span style="font-size:10pt">}</span></div></div><div><span style="font-size:10pt"><br></span></div><div><div><span class="ecxApple-tab-span" style="white-space:pre"> </span>renderingEngine->saveCurrentSettings();</div><br class="ecxApple-interchange-newline"></div><div>Basically I want my 3 channel image to be red, green, blue....</div><div>However the first two channels appear as white, whilst only the last is blue... I tried moving the <span style="font-size:10pt">saveCurrentSettings() after each channel call, but no joy.</span></div><div><span style="font-size:10pt">I'm sure it's something simple, but can't figure it out... </span></div><div>Thanks in advance,</div><div><br></div><div><span style="font-size:10pt">Jerome.</span></div></div>_______________________________________________<br>ome-devel mailing list<br><a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a><br><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br></div></blockquote></div><br></div></div>_______________________________________________<br>ome-devel mailing list<br>ome-devel@lists.openmicroscopy.org.uk<br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel<br></blockquote></div><br></div></div></div> </div>
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