Pipeline with CorrectIlluminationCalculate is very slow?

I have a pipeline that should do nothing but create an illumination function. I use
the (deprecated) LoadImages module, then CorrectIlluminationCalculate, then a
SaveImages to write a mat-file, thats it. In CorrectIlluminationCalculate I selected
to create the shading function upfront in the first cycle.

When I run in headless mode, the pipeline starts, and then no output is printed
to the screen for several hours, during which CP seems to create the shading function
upfront? So far, so good. But when CP starts printing output when its iterating over all
images, the CorrectIlluminationCalculate module takes ~3sec per image! How can that
be, if the model is already created? Should it not breeze through the images now, and
do basically nothing in CorrectIlluminationCalculate, since the model is created
already?

Sorry Mario,
The functionality to create an illumination correction function on the first cycle is very badly supported - mostly there for legacy and I think in the trunk build, you even get a warning for using it. The problem is that CellProfiler is set up to load one image per cycle and loading all the images breaks the model. You end up having to load everything once again anyway, so the best strategy is to use “All: Across cycles”.

Looking at the code, there is some processing that goes on inside CorrectIlluminationCalculate if you select “All: Across cycles” that happens during each run. I didn’t look at it too closely - it looks like it should be fixed eventually, but I don’t think I will get around to it any time soon.

From your description, it looks like you could use “All: Across cycles” - does that work for you?