(Sorry, I had typed up an answer quite while ago, but I see that it is not here - apologies.) Hope this helps, and please post your properties file if not. CPA simply concatenated the PathName and the FileName columns to get the location of your files, so ensure that they concatenate to a valid path (are they perhaps on a network server that is inaccessible?).Is the “image_path_cols = Image_PathName_…” setting there, and looks correct? If the metadata wasn’t extracted for this, I think it is possible for this setting not to have been written, which you can fix by creating the database column and populating it with the full pathname.Ensure that the object named here is the one you intend to classify! In newer versions of CP you can specify this object, but in older versions the default was chosen to be the last object defined in the pipeline. This can be a very “fragile” file, and inspection is a good sanity check. See the documentation for ExportToDatabase. This can cause the yellow warning in ExportToDatabase, in which case you may want to export to multiple per_object tables. (4) Are all the thumbnails blank in CPA Classifier, or only selected ones? If selected ones, that may indicate that you are outputting multiple objects to a single Per_Object table, in which case there may be a non 1-to-1 relationship between the objects. It is a good idea to look at the data as a sanity check regardless! SQLyog for Windows or SequelPro for Mac) or SQLite databases (e.g. There are free tools to look at MySQL (e.g. (3) Look in your output database for these columns. (2) Are you extracting metadata in LoadImages? If so, then the PathName might not be extracted properly – please see this for some ideas: viewtopic.php?f=14&t=3333&p=9325&hilit=+no+such+column+#p9337 Ensure that there were no error/warning dialogs in running the CellProfiler pipeline (don’t just click “continue”!). (1) An error occurred in CP before the database was generated. The blank thumbnails in CPA mean that an ImageNumber and ObjectNumber pair are being found in the database but there is no data associated (or NULL), or possibly there is something wrong with the Location_X/Y column(s).īut from what you sent the specific error is because CPA cannot find the column “Image_PathName_rawGFP” in your database. If you could post the CPA “.properties” file that would be the most expeditious way for us to help you. Second exception was: ERROR: Database query failed for connection "MainThread"Įxception was: no such column: Image_PathName_rawGFPįile “platemappanel.pyc”, line 449, in OnDClickįile “imagetools.pyc”, line 61, in ShowImageįile “imagetools.pyc”, line 51, in FetchImageįile “dbconnect.pyc”, line 665, in GetFullChannelPathsForImageįile “dbconnect.pyc”, line 512, in execute Query was: "SELECT Image_PathName_rawGFP, Image_FileName_rawGFP FROM Per_Image WHERE ImageNumber IN (6)"įirst exception was: no such column: Image_PathName_rawGFP In addition to the error, the images appear as grey boxes in the classifierĭBException: ERROR: Database query failed for connection “MainThread” and failed to reconnect After running a simple pipeline through CellProfiler, and pulling up the resulting data in CPA, this error appears whenever we try to view the images.
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