NB the classifier in question was generated in CPA 3.0.4. However, now finally successfully running a CP 4.2.4 build, I find that the issue is exactly the same as before. I had hoped that it was related to an error in a previous thread ( Error messages from ClassifyObjects module), so spent a long while slowly convincing cellprofiler and related packages to update themselves to the new and correct state (thank you Rebecca for your previous help - it came in handy again with the error messages that came my way during the update process). Any help would be appreciated!įor reference, I originally found this while running a cellprofiler 4.2.1 build. I have only run into this issue on 1 image set out of a batch of 150, but it won’t be sustainable for me to keep rerunning analyses when they randomly fail as a result of this, especially as I have to use ExportToSpreadsheet (export to database is bugged AFAIK when using model-based ClassifyObjects) and a run failing means all data up to that point is lost. Hi, is this issue expected to be resolved now? I am running into the same issue and am struggling to find a fix. Maybe a pretty basic question, but is RandomForest/SVC/KNeighbors applicable in CellProfiler when there are 0.00 values? Or is there something else obvious I am probably missing? RandomForest not dealing well with missing values, but it didn’t seem to be an issue in using “Score all” in CP Analyst. I was guessing it might have something to do with ex. The failed subset of my images (and only this subset) have some measurements which are 0.00 (MinorAxisLength, MinFeretDiameter) which are included in the model. “ValueError: Input contains NaN, infinity or a value too large for dtype(‘float32’).” “ValueError: Input contains infinity or a value too large for dtype(‘float64’).” I am able to run “Score all” in cellprofiler analyst for my images without a problem for Random forest, SVC, KNeighbors, and FGB, but when I try to use the classifier in CellProfiler (either in ClassifyObjects or FilterObject) about a third of my images have either of these error messages depending on the classifier I’m using: I’ve read that this was an issue before, but that it has been fixed in the most recent versions of cellprofiler (4.2.1) and analyst (3.0.4) that I am using. I am having trouble applying any classifier model from CellProfiler analyst other than FGB. This is my first post here and I’m pretty new to CellProfiler, so sorry if this isn’t the right place to ask this!
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