def readDSPlateSetting(plateL, confDir, startAtZero = False,
dateFormat='%m%y%d',
default={'Name':"A", 'Medium': "Complet", 'Serum':10},
addPlateWellsToDB=False, indices={'Xenobiotic':3, 'Dose':4}):
'''
Function to go from as many csv files as there are parameters describing plate setup, to a dictionary
The csv file should not contain spaces in the cells
The file 'wells' should contain the information on where physically on the plate the wells with the numbers
are located. The numbers are the numbers as the images are saved.
'''
result = defaultdict(dict)
idL = {}
well_lines_dict = {}
for plate in plateL:
result[plate]={}
idL[plate]={}
#getting where the existing wells are
try:
file_ =open(os.path.join(confDir, "%s.csv" % plate))
well_lines = file_.readlines(); file_.close()
except OSError:
raise OSError("can't find proper file")
else:
well_lines=np.array([line.strip("\n").strip('\t').split("-") for line in well_lines[1:]])
print well_lines
well_lines_dict[plate]=well_lines
nb_col = 24; nb_row=16
if addPlateWellsToDB:
date = datetime.datetime.strptime(plate[2:6]+plate[-2:], dateFormat)
p = Plate(name = plate, date = date, nb_col=nb_col, nb_row=nb_row)
p.save()
# current_parameters = defaultdict(list)
# for parameter in WELL_PARAMETERS:
# print 'Loading %s parameter'%parameter
# try:
# f=open(os.path.join(confDir, "%s_%s.csv" % (plate, parameter)))
# current_lines=f.readlines()[1:]; f.close()
# except IOError:
# pass
# else:
# current_parameters[parameter]=np.array([line.strip("\n").split(",") for line in current_lines]).ravel()
# current_parameters[parameter] = np.delete(current_parameters[parameter],
# np.where(current_parameters[parameter]==''))
for k, line in enumerate(well_lines):
result[plate][k+1]=defaultdict(dict)
for i,param in enumerate(WELL_PARAMETERS):
try:
result[plate][k+1][param]=line[indices[param]].replace(' ', '')
except KeyError:
result[plate][k+1][param]=default[param]
if addPlateWellsToDB:
medium = result[plate][k+1]['Medium']
serum = int(result[plate][k+1]['Serum'])
conds = Cond.objects.filter(medium = medium)
if len(conds)==0:
cond = addConds(medium, serum)
elif len(conds)==1:
if conds[0].serum!=serum:
cond =addConds(medium, serum)
else:
cond = conds[0]
else:
conds = conds.filter(serum =serum)
if len(conds)==0:
cond =addConds(medium, serum)
elif len(conds)>1:
raise
else:
cond = conds[0]
if addPlateWellsToDB and 'Xenobiotic' in WELL_PARAMETERS:
xb = result[plate][k+1]['Xenobiotic']
try:
dose = float(result[plate][k+1]['Dose'].replace(',', '.'))
except ValueError:
#then it means there are letters in the field
try:
dose = float(result[plate][k+1]['Dose'].replace(',', '.')[:-2])
except ValueError:
#then it meants it's an empty field
dose=0
else:
unit = result[plate][k+1]['Dose'][-2:]
if unit=='uM':
dose*=10**(-6)
elif unit=='nM':
dose*=10**(-9)
elif unit=='pM':
dose*=10**(-12)
treatments = Treatment.objects.filter(xb = xb)
if len(treatments)==0:
treatment = addTreatment(xb, dose)
elif len(treatments)==1:
if treatments[0].dose != dose:
treatment = addTreatment(xb, dose)
else:
treatment =treatments[0]
else:
treatments = treatments.filter(dose =dose)
if len(treatments)==0:
treatment = addTreatment(xb, dose)
elif len(treatments)>1:
raise
else:
treatment =treatments[0]
if addPlateWellsToDB:
clone = result[plate][k+1]['Name'].split("_")[0]
w=Well(num=k+1, plate=p, treatment = treatment, clone = clone)
w.save()
#this is how to add many to many relations
w.cond.add(cond); w.save()
idL[plate][k+1]=w.id
if addPlateWellsToDB:
return result, {plate:np.reshape(range(1,nb_col*nb_row+1),(nb_row,nb_col))}, idL
else:
return result,{plate:np.reshape(range(1,nb_col*nb_row+1),(nb_row,nb_col))}, {}
def readXBPlateSetting(plateL, confDir, startAtZero = False,
plateName=None, dateFormat='%d%m%y',
default={'Name':"Cl1", 'Medium': "Indtp", "Serum":10},
addPlateWellsToDB=False):
'''
Function to go from as many csv files as there are parameters describing plate setup, to a dictionary
The csv file should not contain spaces in the cells
The file 'wells' should contain the information on where physically on the plate the wells with the numbers
are located. The numbers are the numbers as the images are saved.
'''
result = defaultdict(dict)
idL = {}
well_lines_dict = {}
for plate in plateL:
result[plate]={}
idL[plate]={}
#getting where the existing wells are
try:
file_ =open(os.path.join(confDir, "%s_Wells.csv" % plate))
well_lines = file_.readlines(); file_.close()
except OSError:
nb_col = 12; nb_row=8
well_lines = np.reshape(range(1,97),(8,12))
else:
well_lines=np.array([line.strip("\n").split(",") for line in well_lines[1:]], dtype=int)
print well_lines
well_lines_dict[plate]=well_lines
try:
a=int(well_lines[0][11])
except:
try:
a = int(well_lines[0][7])
except:
raise AttributeError("Can't find the number of rows")
else:
nb_col=8
else:
nb_col=12
nb_row = len(well_lines) #dire le nb de lignes dans le fichier - mais en fait on a toujours huit colonnes
# #opening file with well names (clone name usually)
# filename = os.path.join(confDir, "%s_Name.csv" % plate)
#
# f=open(filename)
# lines=f.readlines(); f.close()
#
# lines=np.array([line.strip("\n").split(",") for line in lines][1:]).ravel()
# lines = np.delete(lines, np.where(lines==''))
if addPlateWellsToDB:
p = Plate(name = plateName, date = datetime.datetime.strptime(plate.split('_')[0], dateFormat), nb_col=nb_col, nb_row=nb_row)
p.save()
current_parameters = defaultdict(list)
for parameter in WELL_PARAMETERS:
print 'Loading %s parameter'%parameter
try:
f=open(os.path.join(confDir, "%s_%s.csv" % (plate, parameter)))
current_lines=f.readlines()[1:]; f.close()
except IOError:
pass
else:
current_parameters[parameter]=np.array([line.strip("\n").split(",") for line in current_lines]).ravel()
current_parameters[parameter] = np.delete(current_parameters[parameter],
np.where(current_parameters[parameter]==''))
for k in well_lines.ravel():
result[plate][k]=defaultdict(dict)
for i,param in enumerate(WELL_PARAMETERS):
try:
result[plate][k][param]=current_parameters[param][k-1]
except IndexError:
result[plate][k][param]=default[param]
if addPlateWellsToDB:
medium = result[plate][k]['Medium']
serum = int(result[plate][k]['Serum'])
conds = Cond.objects.filter(medium = medium)
if len(conds)==0:
cond = addConds(medium, serum)
elif len(conds)==1:
if conds[0].serum!=serum:
cond =addConds(medium, serum)
else:
cond = conds[0]
else:
conds = conds.filter(serum =serum)
if len(conds)==0:
cond =addConds(medium, serum)
elif len(conds)>1:
raise
else:
cond = conds[0]
if addPlateWellsToDB and 'Xenobiotic' in WELL_PARAMETERS:
xb = result[plate][k]['Xenobiotic']
dose = int(result[plate][k]['Dose'])
treatments = Treatment.objects.filter(xb = xb)
if len(treatments)==0:
treatment = addTreatment(xb, dose)
elif len(treatments)==1:
if treatments[0].dose != dose:
treatment = addTreatment(xb, dose)
else:
treatment =treatments[0]
else:
treatments = treatments.filter(dose =dose)
if len(treatments)==0:
treatment = addTreatment(xb, dose)
elif len(treatments)>1:
raise
else:
treatment =treatments[0]
if addPlateWellsToDB:
clone = result[plate][k]['Name'].split("_")[0]
w=Well(num=k, plate=p, treatment = treatment, clone = clone)
w.save()
#this is how to add many to many relations
w.cond.add(cond); w.save()
idL[plate][k]=w.id
if addPlateWellsToDB:
return result, well_lines_dict, idL
else:
return result,well_lines_dict, {}