Stephane Dallongeville December 9, 2019 at 6:19 pm
This can happen using the C native optimization library, try to disable (uncheck) it through the plugin configuration :
It should resolve your problem 🙂
– StephaneStephane Dallongeville December 6, 2019 at 6:39 pm
You don’t need extra plugin, you only need to have the VTK library to correctly load, which seems to be your case as you can select the 3D VTK view (not possible when library didn’t loaded properly). Also the complete crash you’re experiencing mean the error happen on VTK side (in which case we can’t catch it unfortunately and so everything close suddenly).
Be sure to have a 64 bit java installed. Another requirement is to have a OpenGL2 compatible video card driver but i guess that is your case but sometime updating the graphical card driver may help.
Also when program crashes that way (mean it’s a JVM crash), you should find an hs_err_pid*.log file into the Icy folder, its content may help in understanding what happened.
– StephaneStephane Dallongeville December 6, 2019 at 4:43 pm
Indeed, i think it’s a nice feature too, it’s why you will have it in next version of Icy 🙂 Descriptors will be called “Intersected” and “Contained” representing respectively the number of Intersected ROI(s) and the number of contained ROI(s).
– StephaneStephane Dallongeville December 2, 2019 at 4:59 pm
You can do that indeed but still the XML file will be saved.Stephane Dallongeville December 2, 2019 at 4:18 pm
You have a global setting in Icy preferences for that :
And you can access it by code with
but don’t forget to restore its prior state..
also that means that sequence closed from GUI won’t save their metadata too during that period (as there is no way to disable that feature on a Sequence basis) so use that safely.
Hope that helps 🙂
– StephaneStephane Dallongeville November 26, 2019 at 6:37 pm
Even if the reply come too late, it may still be useful for developers: the plugin needs to implement a specific interface called Block to be compatible with Protocols so it’s up to the developer to do it. Hopefully when you’re using EzPlug, the Protocols implementation should be really fast and straightforward 🙂
– StephaneStephane Dallongeville November 26, 2019 at 3:54 pm
In fact to do that easily using the Color ROI plugin we need to implement a new ROI Descriptor counting the number of enclosed ROI. Currently there is not that kind of ROI Descriptor as Descriptors are supposed to compute a value relative to a specific ROI. Still that’s possible to do as the compute method from ROI descriptor interface receive have the Sequence information to compute its result (to compute intensity value for instance) so we could retrieve all ROI from the Sequence that way. Honestly that is not a very elegant way of doing that, a better way would be to have a new kind of ROI Descriptor computed against a list of ROI. Still at this point, it’s not probably too hurtful to try that (i’m just afraid about the computing time when you have many ROIs in your sequence).
We will probably give a shot about it soon as indeed it would be really useful to have that descriptor (intersected ROI / contained ROI) 🙂
– StephaneStephane Dallongeville November 26, 2019 at 10:35 am
As you probably noticed, the parameter channel is defined as “channel(s)” which means you can specify several channel here. I admit that is not necessary obvious :
As you can see you just need to separate channel index by a space character 😉
– StephaneStephane Dallongeville November 25, 2019 at 4:23 pm
In fact internally you cannot directly add a channel to an image, it will always generate a new Sequence whatever happen so using the combine channel block you reproduce the exact same behavior except that you have to specify which channel(s) you want to keep on your original image.
So in a word, we can add a new “add channel” block but just to tell you it will do the same process as “combine channel” internally.
– StephaneStephane Dallongeville November 25, 2019 at 4:20 pm
I forgot to reply you sorry ! Well about the merge channel block, to be honest it is not really suited to do a protocols block for that, because the input would be a folder and we have no real output except file make that not really straightforward for protocol classical usage. Still it could be in form of a script so we do the merging operation before (and outside) the protocol then execute the protocol on merged images 🙂
About your second question, what you can try is to “convexify” your ROI (you have a block for that) !
– StephaneStephane Dallongeville November 18, 2019 at 6:09 pm
Dear Kyrollos Yanny,
Testing here doesn’t exhibit the problem. Can we have more information about your system (OS, java version, image propertie) ? Also did you updated Java or your graphics card driver recently ?
– StephaneStephane Dallongeville November 12, 2019 at 12:56 pm
We updated both ROI Statistics and Workbook plugin which may fix some weird issues when number of ROI is > 65535 (wasn’t directly due to the size of XLSX file but more to the processing queue size). We also fixed a performance issue during workbook generation when ‘Color’ field was exported. Can you tell us if that fixed your problem ? Thanks.
– StephaneStephane Dallongeville November 8, 2019 at 5:21 pm
Indeed sometime we observe that flickers, i believe it’s dependent from the video card driver. Did you tried to not overlap the VTK rendering without during the 3D rotation execution ? Something you may try as well is to switch in “detached mode” before doing the rendering :
Hope that helps.
– StephaneStephane Dallongeville November 8, 2019 at 4:41 pm
XLSX should be able to handle more than 1 000 000 rows while XLS is limited to 65536 rows maximum.
ROI Statistics export in XLSX format by default, so i don’t understand why it doesn’t work in your case.
Does the problem appears with the ROI Statistics and ROI inclusion analysis plugin or only with the latter ?
In the meantime I will try to replicate the issue.