def runDrop(self, objId, varsToDrop):
import copy
experiment = self.readExperiment(self.inputExperiment.get().fnPKPD)
self.printSection("Dropping variables")
varsToDrop = []
for varName in self.varsToDrop.get().split(','):
varsToDrop.append(varName.strip())
filteredExperiment = PKPDExperiment()
filteredExperiment.general = copy.copy(experiment.general)
filteredExperiment.variables = {}
for varName, variable in experiment.variables.items():
if not varName in varsToDrop:
filteredExperiment.variables[varName] = copy.copy(variable)
filteredExperiment.samples = {}
filteredExperiment.doses = copy.copy(experiment.doses)
for sampleKey, sample in experiment.samples.items():
candidateSample = PKPDSample()
candidateSample.variableDictPtr = filteredExperiment.variables
candidateSample.doseDictPtr = filteredExperiment.doses
candidateSample.sampleName = copy.copy(sample.sampleName)
candidateSample.doseList = copy.copy(sample.doseList)
candidateSample.descriptors = copy.copy(sample.descriptors)
candidateSample.measurementPattern = []
for varName in sample.measurementPattern:
if not varName in varsToDrop:
candidateSample.measurementPattern.append(varName)
exec(
"candidateSample.measurement_%s = copy.copy(sample.measurement_%s)"
% (varName, varName))
filteredExperiment.samples[
candidateSample.varName] = candidateSample
self.writeExperiment(filteredExperiment,
self._getPath("experiment.pkpd"))
self.experiment = filteredExperiment
def runFilter(self, objId, filterType, condition):
import copy
experiment = self.readExperiment(self.inputExperiment.get().fnPKPD)
self.printSection("Filtering")
if self.filterType.get() == 0:
filterType = "exclude"
elif self.filterType.get() == 1:
filterType = "keep"
elif self.filterType.get() == 2:
filterType = "rmNA"
elif self.filterType.get() == 3:
filterType = "rmLL"
elif self.filterType.get() == 4:
filterType = "subsLL"
elif self.filterType.get() == 5:
filterType = "subsUL"
filteredExperiment = PKPDExperiment()
filteredExperiment.general = copy.copy(experiment.general)
filteredExperiment.variables = copy.copy(experiment.variables)
filteredExperiment.samples = {}
filteredExperiment.doses = {}
filteredExperiment.vias = {}
usedDoses = []
for sampleKey, sample in experiment.samples.items():
candidateSample = PKPDSample()
candidateSample.variableDictPtr = copy.copy(sample.variableDictPtr)
candidateSample.doseDictPtr = copy.copy(sample.doseDictPtr)
candidateSample.sampleName = copy.copy(sample.sampleName)
candidateSample.doseList = copy.copy(sample.doseList)
candidateSample.descriptors = copy.copy(sample.descriptors)
candidateSample.measurementPattern = copy.copy(
sample.measurementPattern)
N = 0 # Number of initial measurements
if len(sample.measurementPattern) > 0:
aux = getattr(sample,
"measurement_%s" % sample.measurementPattern[0])
N = len(aux)
if N == 0:
continue
# Create empty output variables
Nvar = len(sample.measurementPattern)
convertToFloat = []
for i in range(0, Nvar):
exec("candidateSample.measurement_%s = []" %
sample.measurementPattern[i])
convertToFloat.append(
sample.variableDictPtr[sample.measurementPattern[i]].
varType == PKPDVariable.TYPE_NUMERIC)
for n in range(0, N):
toAdd = []
okToAddTimePoint = True
conditionPython = copy.copy(condition)
for i in range(0, Nvar):
ldict = {}
exec(
"aux=sample.measurement_%s[%d]" %
(sample.measurementPattern[i], n), locals(), ldict)
aux = ldict['aux']
if filterType == "rmNA":
if aux == "NA" or aux == "None":
okToAddTimePoint = False
else:
toAdd.append(aux)
elif filterType == "rmLL":
if aux == "LLOQ" or aux == "ULOQ":
okToAddTimePoint = False
else:
toAdd.append(aux)
elif filterType == "subsLL":
okToAddTimePoint = True
if aux == "LLOQ":
toAdd.append(str(self.substitute.get()))
else:
toAdd.append(aux)
elif filterType == "subsUL":
okToAddTimePoint = True
if aux == "ULOQ":
toAdd.append(str(self.substitute.get()))
else:
toAdd.append(aux)
else:
# Keep or exclude
toAdd.append(aux)
varString = "$(%s)" % sample.measurementPattern[i]
if varString in conditionPython:
if aux == "NA":
okToAddTimePoint = False
else:
if convertToFloat[i]:
conditionPython = conditionPython.replace(
varString, "%f" % float(aux))
else:
conditionPython = conditionPython.replace(
varString, "'%s'" % aux)
if (filterType == "exclude"
or filterType == "keep") and okToAddTimePoint:
okToAddTimePoint = eval(conditionPython,
{"__builtins__": None}, {})
if filterType == "exclude":
okToAddTimePoint = not okToAddTimePoint
if okToAddTimePoint:
for i in range(0, Nvar):
exec("candidateSample.measurement_%s.append('%s')" %
(sample.measurementPattern[i], toAdd[i]))
N = len(
getattr(sample, "measurement_%s" % sample.measurementPattern[0]
)) # Number of final measurements
if N != 0:
filteredExperiment.samples[
candidateSample.sampleName] = candidateSample
for doseName in candidateSample.doseList:
if not doseName in usedDoses:
usedDoses.append(doseName)
if len(usedDoses) > 0:
for doseName in usedDoses:
filteredExperiment.doses[doseName] = copy.copy(
experiment.doses[doseName])
viaName = experiment.doses[doseName].via.viaName
if not viaName in filteredExperiment.vias:
filteredExperiment.vias[viaName] = copy.copy(
experiment.vias[viaName])
self.writeExperiment(filteredExperiment,
self._getPath("experiment.pkpd"))
self.experiment = filteredExperiment
def runFilter(self, objId, filterType, condition):
import copy
experiment = self.readExperiment(self.inputExperiment.get().fnPKPD)
self.printSection("Filtering")
if self.filterType.get() == 0:
filterType = "exclude"
elif self.filterType.get() == 1:
filterType = "keep"
else:
filterType = "rmNA"
filteredExperiment = PKPDExperiment()
filteredExperiment.general = copy.copy(experiment.general)
filteredExperiment.variables = copy.copy(experiment.variables)
filteredExperiment.vias = copy.copy(experiment.vias)
filteredExperiment.groups = {}
filteredExperiment.samples = {}
filteredExperiment.doses = {}
# http://stackoverflow.com/questions/701802/how-do-i-execute-a-string-containing-python-code-in-python
safe_list = ['descriptors']
safe_dict = dict([(k, locals().get(k, None)) for k in safe_list])
usedDoses = []
for sampleKey, sample in experiment.samples.items():
ok = filterType == "rmNA"
try:
if filterType == "rmNA":
conditionPython = "True"
else:
conditionPython = copy.copy(condition)
conditionPython = conditionPython.replace(
'$(sampleName)', '"%s"' % sample.sampleName)
for key, variable in experiment.variables.items():
if key in sample.descriptors:
value = sample.descriptors[key]
if value == "NA":
conditionPython = "False"
elif value == "NS":
conditionPython = "False"
elif value == "":
conditionPython = "False"
else:
if filterType != "rmNA":
if variable.varType == PKPDVariable.TYPE_NUMERIC:
conditionPython = conditionPython.replace(
"$(%s)" % key,
"%f" % float(sample.descriptors[key]))
else:
conditionPython = conditionPython.replace(
"$(%s)" % key,
"'%s'" % sample.descriptors[key])
ok = eval(conditionPython,
{"__builtins__": {
"True": True,
"False": False
}}, {})
except:
print(sys.exc_info()[0])
pass
if (ok and (filterType == "keep" or filterType == "rmNA")) or (
not ok and filterType == "exclude"):
filteredExperiment.samples[sampleKey] = copy.copy(sample)
for doseName in sample.doseList:
usedDoses.append(doseName)
for groupName in sample.groupList:
if not groupName in filteredExperiment.groups:
filteredExperiment.groups[groupName] = copy.copy(
experiment.groups[groupName])
if len(usedDoses) > 0:
for doseName in usedDoses:
filteredExperiment.doses[doseName] = copy.copy(
experiment.doses[doseName])
self.writeExperiment(filteredExperiment,
self._getPath("experiment.pkpd"))
self.experiment = filteredExperiment