def usable_XBSC(compound, dose, plate=None, input_folder='../data', confDir='/media/lalil0u/New/projects/Xb_screen/protocols_etal/plate_setups'):
_, info_dict=fromXBToWells([compound], dose_filter=dose, plate=plate,confDir=confDir)
print "Loading manual quality control results"
f=open(os.path.join(input_folder, 'xb_manual_qc.pkl'), 'r')
d_manual=pickle.load(f)
f.close()
print "Loading automatic out of focus and cell count quality control results"
f=open(os.path.join(input_folder, 'xb_focus_qc.pkl'), 'r')
flou_qc=pickle.load(f)
f.close()
expL=[]
if plate is not None:
wells=info_dict[compound][dose][plate]
for well in wells:
if ((plate not in flou_qc) or (plate in flou_qc and well not in flou_qc[plate])):
if ((plate not in d_manual) or (plate in d_manual and well not in d_manual[plate])):
expL.append((plate, '{:>05}'.format(well)))
else:
for plate in info_dict[compound][dose]:
wells=info_dict[compound][dose][plate]
for well in wells:
if ((plate not in flou_qc) or (plate in flou_qc and well not in flou_qc[plate])):
if ((plate not in d_manual) or (plate in d_manual and well not in d_manual[plate])):
expL.append((plate, '{:>05}'.format(well)))
return expL
def computingToRedo(threshold_flou=0.37, threshold_init_cell_count=23, threshold_control_count=3,
input_folder='../data',
hdf5Folder = "/media/lalil0u/New/projects/Xb_screen/plates__all_features_2bis",
savingFolder = "/media/lalil0u/New/projects/Xb_screen/dry_lab_results",
verbose=False):
'''
What should the goal of this function be?
I have a list of xenobiotics and doses and I want to know if I have three experiments on a different day for each
ALSO
the number of experiments discarded by this qc rule
ALSO
normally there are five controls/solvent/plate. There should not be less than three otherwise the plate is to be discarded (oh god)
'''
print 'Counting experiments starting with plates ', plates
failed=defaultdict(dict); passed=defaultdict(dict)
number_failed=0; total_number=0
flou_qc_dict=defaultdict(list)
_,well_groups=fromXBToWells(compoundL)
who=[]; qc_indicators = np.empty(shape=(total_experiment_number,3), dtype=float); qc_indicators.fill(-1)
print "Loading manual quality control results"
f=open(os.path.join(input_folder, 'xb_manual_qc.pkl'), 'r')
d_manual=pickle.load(f)
f.close()
result=defaultdict(dict)
for plate in plates:
f=open(os.path.join(savingFolder, 'processedDictResult_P{}.pkl'.format(plate)))
resCour=pickle.load(f)
f.close()
result[plate]=resCour
for compound in compoundL:
print "################################# Loading wells for xenobiotic ", compound
#by default this function returns all wells with this xenobiotic starting on the 20th of Nov
curr_well_groups=well_groups[compound]
failed[compound]=defaultdict(list)
passed[compound]=defaultdict(list)
for dose in curr_well_groups:
print "----DOSE ", dose
total_bio_replicates=0; total_num_wells=0
for plate in curr_well_groups[dose]:
usable_plate=False
for well in curr_well_groups[dose][plate]:
total_number+=1
print plate, well; who.append((plate, well, compound, dose))
#i.checking if the well is in the manual qc failed list
if plate in d_manual and well in d_manual[plate]:
print 'Manual QC failed', plate, well
failed[compound][dose].append((plate, well))
number_failed+=1
else:
#ii. checking if the initial number of objects is above the threshold
try:
avg_init_cell_count=np.mean(np.array(result[plate][well]['cell_count'])[:10])
except ValueError:
print " MISSING INFO "
continue
if verbose:
print "Avg init cell count ", avg_init_cell_count
qc_indicators[total_number-1, 0]=avg_init_cell_count
avg_init_cell_perc=np.mean((np.array(result[plate][well]['cell_count'], dtype=float)/np.array(result[plate][well]['object_count']))[:10])
if verbose:
print "Avg init cell perc ", avg_init_cell_perc
qc_indicators[total_number-1, 1]=avg_init_cell_perc
flou_arr=np.array(result[plate][well]['Flou_ch1'])
end_flou_perc=np.mean(flou_arr[min(190, flou_arr.shape[0]-10):min(200, flou_arr.shape[0])])
if verbose:
print "Avg end out of focus perc ", end_flou_perc
qc_indicators[total_number-1, 2]=end_flou_perc
if avg_init_cell_count<threshold_init_cell_count:
if verbose:
print 'Cell count failed', plate, well
failed[compound][dose].append((plate, well))
number_failed+=1
flou_qc_dict[plate].append(well)
#iii. checking if the percentage of out of focus objects in the last frames is ok
elif end_flou_perc>threshold_flou:
if verbose:
print 'Out of focus count failed', plate, well
failed[compound][dose].append((plate, well))
number_failed+=1
flou_qc_dict[plate].append(well)
else:
passed[compound][dose].append((plate,well))
usable_plate=True
total_num_wells+=1
if usable_plate:
total_bio_replicates+=1
print '****number of wells ', total_num_wells
print '*****************************biological rep ', total_bio_replicates
print 'Saving list of failed wells in ', os.path.join(input_folder, 'xb_focus_qc.pkl')
f=open(os.path.join(input_folder, 'xb_focus_qc.pkl'), 'w')
pickle.dump(flou_qc_dict, f); f.close()
print "Percentage of experiments failed ", number_failed/float(total_number)
return passed, failed, number_failed, np.hstack((np.array(who), qc_indicators))
