def __init__(self, absorbanses, parent=None):
super(Plate, self).__init__(parent)
self.absorbanses = absorbanses
self.concentrations = np.empty(self.plateSize)
self.concentrations[:]=np.NAN
self.approximation = None
self.reference = Reference()
self.notes = None
self.dirty = False
def loadFromFile(cls, fileName):
'''
Read plate file and return list of plate records, or empty list if reading was unsucsessfull
'''
def wellFromLine(line):
column = int(line[1:])-1
row = ord(line[0])-ord('A')
return row,column
plateFile = open(unicode(fileName))
caption = plateFile.readline().strip()
if caption.startswith(cls.inputTitle) :
print('Loading plate from txt')
plateNumber = 1
absorbanses = np.empty(cls.plateSize)
absorbanses[:]=np.NAN
plates = []
print('parsing plate',plateNumber)
while True:
line = plateFile.readline().split()
isEndFile=not line[0].isdigit()
if isEndFile or (int(line[0])>plateNumber) : # writing plate record
plate = cls(absorbanses)
plates.append(plate)
print('Loaded plate absorbances')
print(absorbanses)
if isEndFile:
break
plateNumber+=1
absorbanses = np.zeros(cls.plateSize)
print('parsing plate',plateNumber)
wellline=line[2]
row,column = wellFromLine(wellline)
absorbanses[row, column] = float(line[-1])
line = ''
while not line.strip() == 'Protocol description':
line = plateFile.readline()
notes = plateFile.readlines()
for plate in plates :
plate.notes=notes
return plates
elif caption == cls.outputTitle :
print('Loading plate from ElisaSolver csv')
plateFile.readline()
plateFile.readline()
absorbanses=cls.readTable(plateFile)
plate = cls(absorbanses)
plateFile.readline()
appName = plateFile.readline().split(':')[1].strip()
index= indexByName(appName)
plate.setApproximation(index)
plateFile.readline()
strP = plateFile.readline().strip()
if strP != '' :
p = np.array([float(item) for item in strP.split(';')])
else:
p=None
plate.reference=Reference.loadFromFile(plateFile)
print('Reference cells: ',plate.reference)
plateFile.readline()
plateFile.readline()
plate.concentrations= cls.readTable(plateFile)
plate.notes = plateFile.readlines()
print('Approximation: ',plate.approximation.name)
plate.approximation.p = p
print('Coefficients: ',p)
plate.dirty = False
return [plate]
else :
return []
def openReference(self, fileName):
referenceFile = open(unicode(fileName))
reference = Reference.loadFromFile(referenceFile)
if reference is not None :
self.setReference(reference)
referenceFile.close()
class Plate(QtCore.QObject):
'''
Holds and handles all data for single plate --
absorbtions, reference, approximation, concentration
'''
plateSizeRows = 8
plateSizeColumns = 12
plateSize=(plateSizeRows,plateSizeColumns)
inputTitle = 'Plate'
outputTitle = 'ElisaSolver plate output'
formats = ['txt','csv']
signalPlateUpdated = QtCore.pyqtSignal() # Updated all plate
signalWellUpdated = QtCore.pyqtSignal(int,int) # Updated all plate
signalApproximationFitted = QtCore.pyqtSignal(bool)
signalApplyReference = QtCore.pyqtSignal(object)
def __init__(self, absorbanses, parent=None):
super(Plate, self).__init__(parent)
self.absorbanses = absorbanses
self.concentrations = np.empty(self.plateSize)
self.concentrations[:]=np.NAN
self.approximation = None
self.reference = Reference()
self.notes = None
self.dirty = False
def __getitem__(self, index):
'''
return esWell from plate
'''
well = Well(self.absorbanses[index], self.concentrations[index])
if index in self.reference.keys() :
well.setWellType(Well.wellTypeReference)
well.setConcentration(self.reference[index])
return well
def __setitem__(self, index, well):
'''
Store esWell in plate
'''
if self.isWellEmpty(*index):
return
if well.wellType == Well.wellTypeReference :
self.reference[index]=well.concentration
else:
self.reference.remove(index)
self.signalWellUpdated.emit(*index)
def isWellEmpty(self, row,column):
return np.isnan(self.absorbanses[row,column])
def resetApproximation(self):
'''
Clear approximation coefficients and calculated concentrations
'''
self.approximation.p = None
self.concentrations[:]=np.NAN
self.dirty=True
self.signalPlateUpdated.emit()
self.signalApproximationFitted.emit(False)
@classmethod
def readTable(cls, plateFile):
'''
read One plate record from IOStream
'''
lines = []
plateFile.readline()
for i in range(cls.plateSizeRows):
lines.append(plateFile.readline())
c = StringIO('\n'.join(lines))
return np.loadtxt(c,delimiter=';')
@classmethod
@QtCore.pyqtSlot(QtCore.QString)
def loadFromFile(cls, fileName):
'''
Read plate file and return list of plate records, or empty list if reading was unsucsessfull
'''
def wellFromLine(line):
column = int(line[1:])-1
row = ord(line[0])-ord('A')
return row,column
plateFile = open(unicode(fileName))
caption = plateFile.readline().strip()
if caption.startswith(cls.inputTitle) :
print('Loading plate from txt')
plateNumber = 1
absorbanses = np.empty(cls.plateSize)
absorbanses[:]=np.NAN
plates = []
print('parsing plate',plateNumber)
while True:
line = plateFile.readline().split()
isEndFile=not line[0].isdigit()
if isEndFile or (int(line[0])>plateNumber) : # writing plate record
plate = cls(absorbanses)
plates.append(plate)
print('Loaded plate absorbances')
print(absorbanses)
if isEndFile:
break
plateNumber+=1
absorbanses = np.zeros(cls.plateSize)
print('parsing plate',plateNumber)
wellline=line[2]
row,column = wellFromLine(wellline)
absorbanses[row, column] = float(line[-1])
line = ''
while not line.strip() == 'Protocol description':
line = plateFile.readline()
notes = plateFile.readlines()
for plate in plates :
plate.notes=notes
return plates
elif caption == cls.outputTitle :
print('Loading plate from ElisaSolver csv')
plateFile.readline()
plateFile.readline()
absorbanses=cls.readTable(plateFile)
plate = cls(absorbanses)
plateFile.readline()
appName = plateFile.readline().split(':')[1].strip()
index= indexByName(appName)
plate.setApproximation(index)
plateFile.readline()
strP = plateFile.readline().strip()
if strP != '' :
p = np.array([float(item) for item in strP.split(';')])
else:
p=None
plate.reference=Reference.loadFromFile(plateFile)
print('Reference cells: ',plate.reference)
plateFile.readline()
plateFile.readline()
plate.concentrations= cls.readTable(plateFile)
plate.notes = plateFile.readlines()
print('Approximation: ',plate.approximation.name)
plate.approximation.p = p
print('Coefficients: ',p)
plate.dirty = False
return [plate]
else :
return []
@QtCore.pyqtSlot(QtCore.QString)
def saveToFile(self, fileName):
'''
Save plate to ElisaSolver csv
'''
print('Saving plate to file: ',fileName)
plateFile = open(unicode(fileName), 'w')
plateFile.write(self.outputTitle+'\n\n')
plateFile.write('Raw absorbanses data:\n')
numbers = ';'.join(['{:8}'.format(i+1) for i in range(12)])+'\n'
plateFile.write(numbers)
np.savetxt(plateFile, self.absorbanses, fmt='%8.3f',delimiter=';')
plateFile.write('\nApproximation type: {}\n'.format(self.approximation.name))
plateFile.write('Coefficients:\n')
if self.approximation.p is not None:
strP='; '.join([str(coef) for coef in self.approximation.p])
else:
strP=''
plateFile.write(strP+'\n')
self.reference.saveToFile(plateFile)
plateFile.write('\nCalculated concentrations:\n')
plateFile.write(numbers)
np.savetxt(plateFile, self.concentrations, fmt='%8.3f',delimiter=';')
if self.notes is not None :
plateFile.writelines(self.notes)
self.dirty = False
def setApproximation(self, index):
'''
Set approximation by index
'''
self.approximation=approximations[index]()
self.resetApproximation()
def prepareCalibration(self):
'''
Form the list of x and y data from calibration
'''
if self.reference.isEmpty() :
print('No reference cells selected')
return [],[]
print('Preparing calibration...')
print('Reference cells: ',self.reference)
wellsByConc = {}
for index,concentration in self.reference.iteritems() :
absorbance = self.absorbanses[index]
rConc=round(concentration,2)
if rConc not in wellsByConc.keys() :
wellsByConc[rConc]=[absorbance]
else :
wellsByConc[rConc].append(absorbance)
x = [conc for conc in wellsByConc.keys()]
x.sort()
print('Reference data:')
print(x)
y = []
for conc in x :
yList=wellsByConc[conc]
y.append(sum(yList)/len(yList))
print(y)
return x,y
def fitCoefficients(self):
'''
Fit approximation coefficients according to current calibration
'''
x,y = self.prepareCalibration()
if len(x)<self.approximation.referenceCount :
print('Reference list is too short ',len(x))
print('Need at least ',self.approximation.referenceCount)
return None
x = np.array(x)
y = np.array(y)
self.approximation.fitPvals(x,y)
self.dirty=True
self.signalApproximationFitted.emit(True)
return self.approximation.fitPlot
def calculateConcentrations(self):
'''
Calculate concentrations according to current calibration
'''
if not self.approximation.isFitted():
return
print('Calculating concentrations:')
for row in range(self.plateSizeRows):
for column in range(self.plateSizeColumns):
if not self.isWellEmpty(row, column) :
self.concentrations[row,column]=self.approximation.invEval(self.absorbanses[row,column])
self.dirty = True
self.signalPlateUpdated.emit()
@QtCore.pyqtSlot(QtCore.QString)
def openReference(self, fileName):
referenceFile = open(unicode(fileName))
reference = Reference.loadFromFile(referenceFile)
if reference is not None :
self.setReference(reference)
referenceFile.close()
@QtCore.pyqtSlot(QtCore.QString)
def saveReference(self, fileName):
referenceFile = open(unicode(fileName),'w')
self.reference.saveToFile(referenceFile)
referenceFile.close()
def setReference(self, reference):
self.reference = reference
self.resetApproximation()
def applyToAll(self):
'''
Send curent reference with signal signalApplyReference
'''
if not self.reference.isEmpty():
self.signalApplyReference.emit(self.reference)