ewiger
commented
9 years ago Thank you for spotting this Thomas. Indeed, this problem has been fixed, but not deployed. I have tested that it works on Brutus now.
>> check_missing_images_in_folder('/BIOL/sonas/biol_uzh_pelkmans_s5/Data/Users/Thomas/150625-RBPoverexpression/TIFF/')
check_missing_images_in_folder: checking /BIOL/sonas/biol_uzh_pelkmans_s5/Data/Users/Thomas/150625-RBPoverexpression/TIFF/
check_missing_images_in_folder: number of images per well (and timepoint) is as follows:
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 126 126 126 126 126 126 126 126 126 126 126 0 0 0 0 0 0 0
0 0 0 0 0 0 126 126 126 126 126 126 126 126 126 126 126 0 0 0 0 0 0 0
0 0 0 0 0 0 126 126 126 126 126 126 126 126 126 126 126 0 0 0 0 0 0 0
0 0 0 0 0 0 126 126 126 126 126 126 126 126 126 126 126 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
check_missing_images_in_folder: dataset looks complete
As part of PreCluster, iBrain used to perform a check for the correct number of images per site (for every channel).
However, now a function appears missing, leading to the skipping of this safety check (note: pipeline will still continue - however mistakes, which do not lead to errors would be possible).
This problem appears related to https://github.com/pelkmanslab/iBRAINShared/issues/11
Example:
< M A T L A B (R) > Copyright 1984-2012 The MathWorks, Inc. R2012b (8.0.0.783) 64-bit (glnxa64) August 22, 2012
To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com.
/cluster/home/biol/yyauhen/iBRAIN/startup.m: randomizing rand initial state /cluster/home/biol/yyauhen/iBRAIN/startup.m: 48 CPUs detected, using 1 threads
Error in check_missing_images_in_folder (line 48) matPlateImagesPerWell(sub2ind([16,24,max(matTimePoints)],iPos(:,1),iPos(:,2),iPos(:,3))) = countNumberOfValues(n); }