TypeError in CPA when trying to fetch classified objects, & object thumbnail random fail to load

cellprofiler
cellprofiler-analyst

#1

Hi,

I’m facing a couple of errors with CPA.

The first is similar to an error reported previously (https://github.com/CellProfiler/CellProfiler-Analyst/issues/178).

However unlike that situation, I cannot see any “None” type items in my database. Also, I can score the whole image, I just get this error when trying to fetch “classified” objects if I use anything except Fast Gentle Boosting:

"An error occurred in the program:
TypeError: ufunc ‘isinf’ not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ‘‘safe’’

Traceback (most recent call last):
File “cpa\classifier.pyc”, line 989, in OnFetch
File “cpa\generalclassifier.pyc”, line 78, in FilterObjectsFromClassN
File “cpa\multiclasssql.pyc”, line 127, in FilterObjectsFromClassN
File “cpa\multiclasssql.pyc”, line 157, in processData
File “numpy\lib\type_check.pyc”, line 374, in nan_to_num
File “numpy\lib\ufunclike.pyc”, line 113, in isposinf"

The second problem is that thumbnails of objects will randomly fail to load when I’m trying to fetch objects. Normally after 5-10 objects have appeared, but sometimes up to 80 object images will load before they just show a blank image.

I can’t upload my database here, but could drop off somewhere should anyone wish to see it.

Warm regards,

Ed

1002.cpproj (147.1 KB)

1002.properties (7.1 KB)
1002.properties (7.1 KB)


#2

Hi,

Your first bug is a known one that’s fixed in the source version of CPA, if you’re able and willing to solve that.

The latter I’m guessing could be a memory issue, does the full image pop up when you double click on the thumbnail or do you get some sort of an error?


#3

Hi,

Thanks I’ll try to fix the first error from source and update you on my progress.

The full image does indeed pop up when I double click the thumbnail, if a little slowly.

Best wishes,

Ed


#4

Hi,

I’ve successfully built the latest cellprofiler and cellprofiler analyst versions on my laptop, in order to avoid the issue I was having. However, now CPA freezes when I try to open the properties file. This makes no sense given that the same properties file opens just fine in the stable version. It does however open with other properties files. Could someone take a peak at my properties file and see what could be causing CPA to crash? I’d be very appreciative!

Cheers,
Ed

1001b.properties (7.3 KB)


#5

Hi,

Can you please remove Per_ when you define variables and instead write Image and Object.
image_table = Per_Image
object_table = Per_Object

remove Image_ from each of the following below variables
plate_id = Image_Metadata_Plate
well_id = Image_Metadata_Well
series_id = Image_Group_Number
group_id = Image_Group_Number
timepoint_id = Image_Group_Index

Let me know if this works for you.


#6

Hi Hamdah,

Thanks very much for the suggestion, however unfortunately the program still crashes.

Any other ideas?

Best wishes,

Ed


#7

Can you try setting check_tables to no? That’s unfortunately a known buggy thing.


#8

The good news is that CPA now successfully opens the properties file - thanks!

I’m getting a different error now when training the classifiers, but I’ll start a new thread on that in due course.

Best wishes,

Ed