def loadLandscapeDataAlt(filenames, male=True, female=True, dataType=float):
"""
Description:
* Imports the information of all the nodes within an experiment's
folder.
In:
* filenames: Dictionary with male/female filenames.
Out:
* Dictionary containing:
"genotypes" [list -> strings]
"landscape" [list -> numpyArrays]
Notes:
* NA
"""
maleFilesNumber = len(filenames["male"])
femaleFilesNumber = len(filenames["female"])
maleFilesEqualFemales = (maleFilesNumber == femaleFilesNumber)
filesExist = (maleFilesNumber >= 1 and femaleFilesNumber >= 1)
# Select the appropriate aggregation scheme: male+female, male, female
if (male and female) and maleFilesEqualFemales and filesExist:
maleFilenames = filenames["male"]
femaleFilenames = filenames["female"]
genotypes = auxFun.readGenotypes(maleFilenames[0])
nodesDataList = [None] * maleFilesNumber
for i in range(0, maleFilesNumber):
nodesDataList[i] = loadNodeDataAlt(maleFilenames[i],
femaleFilenames[i],
dataType=dataType)["population"]
returnDictionary = {"genotypes": genotypes, "landscape": nodesDataList}
return returnDictionary
elif female and femaleFilesNumber >= 1:
femaleFilenames = filenames["female"]
genotypes = auxFun.readGenotypes(femaleFilenames[0])
nodesDataList = [None] * femaleFilesNumber
for i in range(0, femaleFilesNumber):
nodesDataList[i] = loadNodeDataAlt(None,
femaleFilenames[i],
dataType=dataType)["population"]
returnDictionary = {"genotypes": genotypes, "landscape": nodesDataList}
return returnDictionary
elif male and maleFilesNumber >= 1:
maleFilenames = filenames["male"]
genotypes = auxFun.readGenotypes(maleFilenames[0])
nodesDataList = [None] * maleFilesNumber
for i in range(0, maleFilesNumber):
nodesDataList[i] = loadNodeDataAlt(maleFilenames[i],
None,
dataType=dataType)["population"]
returnDictionary = {"genotypes": genotypes, "landscape": nodesDataList}
return returnDictionary
else:
warnings.warn(
'''No data was loaded because both male and female filenames
are: None; or there are no files to load.''', Warning)
return None
def loadLandscapeDataEpi(
filenames,
male=True,
female=True,
dataType=float
):
"""
Description:
* Imports the information of all the nodes in filenames
In:
* filenames: List of paths to desired csv files
Out:
* Dictionary containing:
"genotypes" [list -> strings]
"landscape" [list -> numpyArrays]
"""
if len(filenames) == 0:
return
genotypes = auxFun.readGenotypes(filenames[0])
nodesDataList = []
for f in filenames:
data = loadNodeDataEpi(f, dataType)["population"]
nodesDataList.append(data)
returnDictionary = {
"genotypes": genotypes,
"landscape": nodesDataList
}
return returnDictionary
def loadNodeDataEpi(
filename,
dataType=float,
skipHeader=1,
skipColumns=1
):
"""
Description:
* Loads the data given by filename
In:
* filename: path to csv file
* dataType: To save memory/processing time if possible (int/float).
Out:
* Dictionary containing:
"genotypes" [list -> strings]
"population" [numpyArray]
"""
genotypes = auxFun.readGenotypes(filename)
data = np.genfromtxt(
filename,
dtype=dataType,
skip_header=skipHeader,
delimiter=",")
returnDictionary = {
"genotypes": genotypes,
"population": data[:, skipColumns:]
}
return returnDictionary
def loadNodeDataAlt(maleFilename=None,
femaleFilename=None,
dataType=float,
skipHeader=1,
skipColumns=1):
"""
Description:
* Loads the data for a single node in the files. If male and female
filenames are provided, it sums them as a matrix operation.
Avoids the use of np.readfromtxt, to avoid the overhead
In:
* maleFilename: Path to the male CSV file to process.
* femaleFilename: Path to the female CSV file to process.
* dataType: To save memory/processing time if possible (int/float).
Out:
* Dictionary containing:
"genotypes" [list -> strings]
"population" [numpyArray]
Notes:
* Timing information is dropped.
"""
if (maleFilename is not None) and (femaleFilename is not None):
genotypes = auxFun.readGenotypes(maleFilename)
dataM = fileReader(maleFilename,
dtype=dataType,
skipHeader=skipHeader,
skipColumns=skipColumns)
dataF = fileReader(femaleFilename,
dtype=dataType,
skipHeader=skipHeader,
skipColumns=skipColumns)
if dataM.shape[0] > dataF.shape[0]:
returnDictionary = {
"genotypes": genotypes,
"population": (np.resize(dataM, dataF.shape) + dataF)
}
else:
returnDictionary = {
"genotypes": genotypes,
"population": (dataM + np.resize(dataF, dataM.shape))
}
return returnDictionary
elif femaleFilename is not None:
genotypes = auxFun.readGenotypes(femaleFilename)
dataF = fileReader(femaleFilename,
dtype=dataType,
skipHeader=skipHeader,
skipColumns=skipColumns)
returnDictionary = {"genotypes": genotypes, "population": dataF}
return returnDictionary
elif maleFilename is not None:
genotypes = auxFun.readGenotypes(maleFilename)
dataM = fileReader(maleFilename,
dtype=dataType,
skipHeader=skipHeader,
skipColumns=skipColumns)
returnDictionary = {"genotypes": genotypes, "population": dataM}
return returnDictionary
else:
warnings.warn(
'''No data was loaded because both male and female filenames
are: None''', Warning)
return None