Closed bethac07 closed 2 years ago
Is it easy/possible to try them out on an example set just to make sure I didn't do anything dumb?
For sure.
Fresh pull on CellProfiler and CellProfiler-plugins. On master branch of CellProfiler-plugins my test pipeline opens fine, but on barcode cleanup
branch I get Error while loading CallBarcodes: Could not find the CallBarcodes module
Works in both test mode and analysis mode if CallBarcodes module does NOT display results. If display is on in either test mode or analysis mode nothing shows in GUI and:
Failed to run module CallBarcodes
Traceback (most recent call last):
File "/Users/eweisbar/Desktop/github/CellProfiler/cellprofiler/gui/pipelinecontroller.py", line 3397, in do_step
module.display(workspace_model, fig)
File "/Users/eweisbar/Desktop/github/CellProfiler-plugins/callbarcodes.py", line 475, in display
figure.subplot_table(0, 0, statistics)
File "/Users/eweisbar/Desktop/github/CellProfiler/cellprofiler/gui/figure/_figure.py", line 2194, in subplot_table
ncols = 0 if nrows == 0 else len(statistics[0])
TypeError: object of type 'numpy.float64' has no len()
Thanks for looking into that! Since it hasn't had a functional display until now, no point holding it for one at this point.
Can you make sure though to add/push the changes you needed to make to get it to run? My recollection is that they were small but nonzero.
Implements an initial check for a perfect barcode match rather than score checking all barcodes, which has only a moderate impact when the barcode list is small but can lead to a 250X speedup when the barcode list is 30K barcodes.
Also adds a few things from a branch too old to be worth rebasing (and which had some features we've since decided we don't want) - 1) allowing the user to set an empty vector barcode and 2) reporting a mean quality score for each barcode foci. It also now exports to the Image measurement table the mean score and the mean quality score for all barcodes in each image, which should make life easier when wanting to do quick checks on how processing went.