from Packages import *
from .Evaluation_Metrics import metrics
## try to automatically detect the field separator within the CSV
def find_delimiter(filename):
import clevercsv
with open(filename, newline='') as csvfile:
delimiter = clevercsv.Sniffer().sniff(csvfile.read(100)).delimiter
# sniffer = csv.Sniffer()
# with open(filename) as fp:
# delimiter = sniffer.sniff(fp.read(200)).delimiter
return delimiter
def find_col_index(filename):
with open(filename) as fp:
lines = pd.read_csv(fp, skiprows=3, nrows=3, index_col=False, sep=find_delimiter(filename))
col_index = 'yes' if lines.iloc[:,0].dtypes != np.float64 else 'no'
return col_index
# detection of columns categories and scaling
def col_cat(data_import):
"""detect numerical and categorical columns in the csv"""
# set first column as sample names
name_col = pd.DataFrame(list(data_import.index), index = list(data_import.index))
# name_col=name_col.rename(columns = {0:'name'})
numerical_columns_list = []
categorical_columns_list = []
for i in data_import.columns:
if data_import[i].dtype == np.dtype("float64") or data_import[i].dtype == np.dtype("int64"):
numerical_columns_list.append(data_import[i])
else:
categorical_columns_list.append(data_import[i])
if len(numerical_columns_list) == 0:
empty = [0 for x in range(len(data_import))]
numerical_columns_list.append(empty)
if len(categorical_columns_list) > 0:
categorical_data = pd.concat(categorical_columns_list, axis=1)
categorical_data.insert(0, 'name', name_col)
if len(categorical_columns_list) == 0:
categorical_data = pd.DataFrame
# Create numerical data matrix from the numerical columns list and fill na with the mean of the column
numerical_data = pd.concat(numerical_columns_list, axis=1)
numerical_data = numerical_data.apply(lambda x: x.fillna(x.mean())) #np.mean(x)))
return numerical_data, categorical_data
def list_files(mypath, import_type):
list_files = [f for f in listdir(mypath) if isfile(join(mypath, f)) and f.endswith(import_type + '.pkl')]
if list_files == []:
list_files = ['Please, create a model before - no model available yet']
return list_files
def standardize(X, center = True, scale = False):
sk = StandardScaler(with_mean=center, with_std = scale)
sc = pd.DataFrame(sk.fit_transform(X), index = X.index, columns = X.columns)
return sc
def MinMaxScale(X):
t = X
sk = MinMaxScaler(feature_range=(0,1))
sc = pd.DataFrame(sk.fit_transform(X), index = t.index, columns = t.columns)
return sc
######################################## Spectral preprocessing
def Detrend(X):
c = detrend(X, axis=-1, type='linear', bp=0, overwrite_data=False)
return c
def Snv(X):
xt = np.array(X).T
c = (xt-xt.mean())/xt.std()
return pd.DataFrame(c.T, index=X.index, columns= X.columns)
def No_transformation(X):
return X
######################################## Cross val split ############################
class KF_CV:
### method for generating test sets index
### KFCV(dict) returns a testset indices/Fold
@staticmethod
def CV(x, y, n_folds:int):
test_folds = {}
folds_name = [f'Fold{i+1}' for i in range(n_folds)]
kf = ks.KFold(n_splits=n_folds, device='cpu')
for i in range(n_folds):
d = []
for _, i_test in kf.split(x, y):
d.append(i_test)
test_folds[folds_name[i]] = d[i]
return test_folds ## returns a tuple where keys are the name of each fold, and the corresponding values is a 1d numpy array filled with indices of test set
### Cross validate the model and return the predictions and samples index
@staticmethod
def cross_val_predictor(model, folds, x, y):
"""" model: the object to be cross-validated,
folds: a tuple where keys are the name of each fold, and the corresponding values is a 1d numpy array filled with indices of test set(from CV method)
x and y: the data used for CV"""
x = np.array(x)
y = np.array(y)
yp = {}
key = list(folds.keys())
n_folds = len(folds.keys())
for i in range(n_folds):
model.fit(np.delete(x, folds[key[i]], axis=0), np.delete(y, folds[key[i]], axis=0))
yp[key[i]] = model.predict(x[folds[key[i]]]) #### predictions/fold
return yp # returns a tuple with keys are names of folds and the corresponding values are the predicted Y/fold
@staticmethod
def meas_pred_eq(y, ypcv, folds):
"""" y: the target variable,
ypcv: a tuple where keys are the name of each fold, and the corresponding values is a 1d numpy array filled with predictions/fold (from cross_val_predictor method)
folds: a tuple where keys are the name of each fold, and the corresponding values is a 1d numpy array filled with indices of test set(from CV method)
x and y: the data used for CV
returns:
two dataframe:
- a n x 4 dataframe containing measured values, predicted values, ols reg equation, and index (n is the total number of samples)
- a 2 x k dataframe containing ols regression coefficients(k is the number of folds)
"""
cvcv = {}
coeff = {}
y = np.array(y)
for i, Fname in enumerate(folds.keys()):
r = pd.DataFrame()
r['Predicted'] = ypcv[Fname]
r['Measured'] = y[folds[Fname]]
ols = LinearRegression().fit(pd.DataFrame(y[folds[Fname]]), ypcv[Fname].reshape(-1,1))
r.index = folds[Fname]
r['Folds'] = [f'{Fname} (Predicted = {np.round(ols.intercept_[0], 2)} + {np.round(ols.coef_[0][0],2)} x Measured'] * r.shape[0]
cvcv[i] = r
coeff[Fname] = [ols.coef_[0][0], ols.intercept_[0]]
data = pd.concat(cvcv, axis = 0)
data['index'] = [data.index[i][1] for i in range(data.shape[0])]
data.index = data['index']
coeff = pd.DataFrame(coeff, index = ['Slope', 'Intercept'])
return data, coeff ## returns values predicted in cross validation, ,coefficients of regression
@staticmethod
def metrics_cv(y, ypcv, folds):
y = np.array(y)
e = {}
for i in folds.keys():
e[i] = metrics().reg_(y[folds[i]],ypcv[i])
r = pd.DataFrame(e)
r_print = r.copy()
r_print['mean'] = r.mean(axis = 1)
r_print['sd'] = r.std(axis = 1)
r_print['cv'] = 100*r.std(axis = 1)/r.mean(axis = 1)
return r.T, r_print.T
### compute metrics for each fold
@staticmethod
def cv_scores(y, ypcv, folds):
""" Takes as input the Y vactor, the tuple of preducted values/fold(from cross_val_predictor method), and the index/fold(from CV method)
and returns two dataframes, the first is containing metrics scores/fold and the second is similar to the first by with additional mean, sd, and rsd variables
"""
y = np.array(y)
e = {}
for i in folds.keys():
e[i] = metrics().reg_(y[folds[i]],ypcv[i])
r = pd.DataFrame(e)
r_print = r
r_print['mean'] = r.mean(axis = 1)
r_print['sd'] = r.std(axis = 1)
r_print['cv'] = 100*r.std(axis = 1)/r.mean(axis = 1)
return r.T, r_print.T
# ### Return ycv
# @staticmethod
# def ycv(model, x, y, n_folds:int):
# ycv = np.zeros(y.shape[0])
# f, idx,_,_ = KF_CV.cross_val_predictor(model, x,y, n_folds)
# for i in f.keys():
# ycv[idx[i]] = f[i]
# return ycv
### Selectivity ratio
def sel_ratio(model, x ):
from scipy.stats import f
x = pd.DataFrame(x)
wtp = model.coef_.T/ np.linalg.norm(model.coef_.T)
ttp = np.array(x @ wtp)
ptp = np.array(x.T) @ np.array(ttp)/(ttp.T @ ttp)
qexpi = np.linalg.norm(ttp @ ptp.T, axis = 0)**2
e = np.array(x-x.mean()) - ttp @ ptp.T
qres = np.linalg.norm(e, axis = 0)**2
sr = pd.DataFrame(qexpi/qres, index = x.columns, columns = ['sr'])
fcr = f.ppf(0.05, sr.shape[0]-2, sr.shape[0]-3)
c = sr > fcr
sr.index = np.arange(x.shape[1])
SR = sr.iloc[c.to_numpy(),:]
return SR