def save_results(respfile, Yhat, S2, maskvol, Z=None, outputsuffix=None,
results=None, save_path=''):
print("Writing outputs ...")
if respfile is None:
exfile = None
file_ext = '.pkl'
else:
if fileio.file_type(respfile) == 'cifti' or \
fileio.file_type(respfile) == 'nifti':
exfile = respfile
else:
exfile = None
file_ext = fileio.file_extension(respfile)
if outputsuffix is not None:
ext = str(outputsuffix) + file_ext
else:
ext = file_ext
fileio.save(Yhat, os.path.join(save_path, 'yhat' + ext), example=exfile,
mask=maskvol)
fileio.save(S2, os.path.join(save_path, 'ys2' + ext), example=exfile,
mask=maskvol)
if Z is not None:
fileio.save(Z, os.path.join(save_path, 'Z' + ext), example=exfile,
mask=maskvol)
if results is not None:
for metric in list(results.keys()):
fileio.save(results[metric], os.path.join(save_path, metric + ext),
example=exfile, mask=maskvol)
def estimate(respfile,
covfile,
maskfile=None,
cvfolds=None,
testcov=None,
testresp=None,
alg='gpr',
configparam=None,
saveoutput=True,
outputsuffix=None):
""" Estimate a normative model
This will estimate a model in one of two settings according to the
particular parameters specified (see below):
* under k-fold cross-validation
required settings 1) respfile 2) covfile 3) cvfolds>2
* estimating a training dataset then applying to a second test dataset
required sessting 1) respfile 2) covfile 3) testcov 4) testresp
* estimating on a training dataset ouput of forward maps mean and se
required sessting 1) respfile 2) covfile 3) testcov
The models are estimated on the basis of data stored on disk in ascii or
neuroimaging data formats (nifti or cifti). Ascii data should be in
tab or space delimited format with the number of subjects in rows and the
number of variables in columns. Neuroimaging data will be reshaped
into the appropriate format
Basic usage::
estimate(respfile, covfile, [extra_arguments])
where the variables are defined below. Note that either the cfolds
parameter or (testcov, testresp) should be specified, but not both.
:param respfile: response variables for the normative model
:param covfile: covariates used to predict the response variable
:param maskfile: mask used to apply to the data (nifti only)
:param cvfolds: Number of cross-validation folds
:param testcov: Test covariates
:param testresp: Test responses
:param alg: Algorithm for normative model
:param configparam: Parameters controlling the estimation algorithm
:param saveoutput: Save the output to disk? Otherwise returned as arrays
:param outputsuffix: Text string to add to the output filenames
All outputs are written to disk in the same format as the input. These are:
:outputs: * yhat - predictive mean
* ys2 - predictive variance
* Hyp - hyperparameters
* Z - deviance scores
* Rho - Pearson correlation between true and predicted responses
* pRho - parametric p-value for this correlation
* rmse - root mean squared error between true/predicted responses
* smse - standardised mean squared error
The outputsuffix may be useful to estimate multiple normative models in the
same directory (e.g. for custom cross-validation schemes)
"""
# load data
print("Processing data in " + respfile)
X = fileio.load(covfile)
Y, maskvol = load_response_vars(respfile, maskfile)
if len(Y.shape) == 1:
Y = Y[:, np.newaxis]
if len(X.shape) == 1:
X = X[:, np.newaxis]
Nmod = Y.shape[1]
if testcov is not None:
# we have a separate test dataset
Xte = fileio.load(testcov)
testids = range(X.shape[0], X.shape[0] + Xte.shape[0])
if len(Xte.shape) == 1:
Xte = Xte[:, np.newaxis]
if testresp is not None:
Yte, testmask = load_response_vars(testresp, maskfile)
if len(Yte.shape) == 1:
Yte = Yte[:, np.newaxis]
else:
sub_te = Xte.shape[0]
Yte = np.zeros([sub_te, Nmod])
# treat as a single train-test split
splits = CustomCV((range(0, X.shape[0]), ), (testids, ))
Y = np.concatenate((Y, Yte), axis=0)
X = np.concatenate((X, Xte), axis=0)
# force the number of cross-validation folds to 1
if cvfolds is not None and cvfolds != 1:
print("Ignoring cross-valdation specification (test data given)")
cvfolds = 1
else:
# we are running under cross-validation
splits = KFold(n_splits=cvfolds)
testids = range(0, X.shape[0])
# find and remove bad variables from the response variables
# note: the covariates are assumed to have already been checked
nz = np.where(
np.bitwise_and(np.isfinite(Y).any(axis=0),
np.var(Y, axis=0) != 0))[0]
# Initialise normative model
nm = norm_init(X, alg=alg, configparam=configparam)
# run cross-validation loop
Yhat = np.zeros_like(Y)
S2 = np.zeros_like(Y)
Hyp = np.zeros((Nmod, nm.n_params, cvfolds))
Z = np.zeros_like(Y)
nlZ = np.zeros((Nmod, cvfolds))
for idx in enumerate(splits.split(X)):
fold = idx[0]
tr = idx[1][0]
te = idx[1][1]
# standardize responses and covariates, ignoring invalid entries
iy, jy = np.ix_(tr, nz)
mY = np.mean(Y[iy, jy], axis=0)
sY = np.std(Y[iy, jy], axis=0)
Yz = np.zeros_like(Y)
Yz[:, nz] = (Y[:, nz] - mY) / sY
mX = np.mean(X[tr, :], axis=0)
sX = np.std(X[tr, :], axis=0)
Xz = (X - mX) / sX
# estimate the models for all subjects
for i in range(0, len(nz)): # range(0, Nmod):
print("Estimating model ", i + 1, "of", len(nz))
try:
nm = norm_init(Xz[tr, :],
Yz[tr, nz[i]],
alg=alg,
configparam=configparam)
Hyp[nz[i], :, fold] = nm.estimate(Xz[tr, :], Yz[tr, nz[i]])
yhat, s2 = nm.predict(Xz[tr, :], Yz[tr, nz[i]], Xz[te, :],
Hyp[nz[i], :, fold])
Yhat[te, nz[i]] = yhat * sY[i] + mY[i]
S2[te, nz[i]] = s2 * sY[i]**2
nlZ[nz[i], fold] = nm.neg_log_lik
if testcov is None:
Z[te, nz[i]] = (Y[te, nz[i]] - Yhat[te, nz[i]]) / \
np.sqrt(S2[te, nz[i]])
else:
if testresp is not None:
Z[te, nz[i]] = (Y[te, nz[i]] - Yhat[te, nz[i]]) / \
np.sqrt(S2[te, nz[i]])
except Exception as e:
exc_type, exc_obj, exc_tb = sys.exc_info()
fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
print("Model ", i + 1, "of", len(nz),
"FAILED!..skipping and writing NaN to outputs")
print("Exception:")
print(e)
print(exc_type, fname, exc_tb.tb_lineno)
Hyp[nz[i], :, fold] = float('nan')
Yhat[te, nz[i]] = float('nan')
S2[te, nz[i]] = float('nan')
nlZ[nz[i], fold] = float('nan')
if testcov is None:
Z[te, nz[i]] = float('nan')
else:
if testresp is not None:
Z[te, nz[i]] = float('nan')
# compute performance metrics
if testcov is None:
MSE = np.mean((Y[testids, :] - Yhat[testids, :])**2, axis=0)
RMSE = np.sqrt(MSE)
# for the remaining variables, we need to ignore zero variances
SMSE = np.zeros_like(MSE)
Rho = np.zeros(Nmod)
pRho = np.ones(Nmod)
iy, jy = np.ix_(testids, nz) # ids for tested samples nonzero values
SMSE[nz] = MSE[nz] / np.var(Y[iy, jy], axis=0)
Rho[nz], pRho[nz] = compute_pearsonr(Y[iy, jy], Yhat[iy, jy])
else:
if testresp is not None:
MSE = np.mean((Y[testids, :] - Yhat[testids, :])**2, axis=0)
RMSE = np.sqrt(MSE)
# for the remaining variables, we need to ignore zero variances
SMSE = np.zeros_like(MSE)
Rho = np.zeros(Nmod)
pRho = np.ones(Nmod)
iy, jy = np.ix_(testids, nz) # ids tested samples nonzero values
SMSE[nz] = MSE[nz] / np.var(Y[iy, jy], axis=0)
Rho[nz], pRho[nz] = compute_pearsonr(Y[iy, jy], Yhat[iy, jy])
# Set writing options
if saveoutput:
print("Writing output ...")
if fileio.file_type(respfile) == 'cifti' or \
fileio.file_type(respfile) == 'nifti':
exfile = respfile
else:
exfile = None
if outputsuffix is not None:
ext = str(outputsuffix) + fileio.file_extension(respfile)
else:
ext = fileio.file_extension(respfile)
# Write output
if testcov is None:
fileio.save(Yhat[testids, :].T,
'yhat' + ext,
example=exfile,
mask=maskvol)
fileio.save(S2[testids, :].T,
'ys2' + ext,
example=exfile,
mask=maskvol)
fileio.save(Z[testids, :].T,
'Z' + ext,
example=exfile,
mask=maskvol)
fileio.save(Rho, 'Rho' + ext, example=exfile, mask=maskvol)
fileio.save(pRho, 'pRho' + ext, example=exfile, mask=maskvol)
fileio.save(RMSE, 'rmse' + ext, example=exfile, mask=maskvol)
fileio.save(SMSE, 'smse' + ext, example=exfile, mask=maskvol)
if cvfolds is None:
fileio.save(Hyp[:, :, 0],
'Hyp' + ext,
example=exfile,
mask=maskvol)
else:
for idx in enumerate(splits.split(X)):
fold = idx[0]
fileio.save(Hyp[:, :, fold],
'Hyp_' + str(fold + 1) + ext,
example=exfile,
mask=maskvol)
else:
if testresp is None:
fileio.save(Yhat[testids, :].T,
'yhat' + ext,
example=exfile,
mask=maskvol)
fileio.save(S2[testids, :].T,
'ys2' + ext,
example=exfile,
mask=maskvol)
fileio.save(Hyp[:, :, 0],
'Hyp' + ext,
example=exfile,
mask=maskvol)
else:
fileio.save(Yhat[testids, :].T,
'yhat' + ext,
example=exfile,
mask=maskvol)
fileio.save(S2[testids, :].T,
'ys2' + ext,
example=exfile,
mask=maskvol)
fileio.save(Z[testids, :].T,
'Z' + ext,
example=exfile,
mask=maskvol)
fileio.save(Rho, 'Rho' + ext, example=exfile, mask=maskvol)
fileio.save(pRho, 'pRho' + ext, example=exfile, mask=maskvol)
fileio.save(RMSE, 'rmse' + ext, example=exfile, mask=maskvol)
fileio.save(SMSE, 'smse' + ext, example=exfile, mask=maskvol)
if cvfolds is None:
fileio.save(Hyp[:, :, 0],
'Hyp' + ext,
example=exfile,
mask=maskvol)
else:
for idx in enumerate(splits.split(X)):
fold = idx[0]
fileio.save(Hyp[:, :, fold],
'Hyp_' + str(fold + 1) + ext,
example=exfile,
mask=maskvol)
else:
if testcov is None:
output = (Yhat[testids, :], S2[testids, :], Hyp, Z[testids, :],
Rho, pRho, RMSE, SMSE)
else:
if testresp is None:
output = (Yhat[testids, :], S2[testids, :], Hyp[testids, :])
else:
output = (Yhat[testids, :], S2[testids, :], Hyp, Z[testids, :],
Rho, pRho, RMSE, SMSE)
return output
def estimate(args):
torch.set_default_dtype(torch.float32)
args.type = 'MT'
print('Loading the input Data ...')
responses = fileio.load_nifti(args.respfile,
vol=True).transpose([3, 0, 1, 2])
response_shape = responses.shape
with open(args.covfile, 'rb') as handle:
covariates = pickle.load(handle)['covariates']
with open(args.testcovfile, 'rb') as handle:
test_covariates = pickle.load(handle)['test_covariates']
if args.mask is not None:
mask = fileio.load_nifti(args.mask, vol=True)
mask = fileio.create_mask(mask, mask=None)
else:
mask = fileio.create_mask(responses[0, :, :, :], mask=None)
if args.testrespfile is not None:
test_responses = fileio.load_nifti(args.testrespfile,
vol=True).transpose([3, 0, 1, 2])
test_responses_shape = test_responses.shape
print('Normalizing the input Data ...')
covariates_scaler = StandardScaler()
covariates = covariates_scaler.fit_transform(covariates)
test_covariates = covariates_scaler.transform(test_covariates)
response_scaler = MinMaxScaler()
responses = unravel_2D(response_scaler.fit_transform(ravel_2D(responses)),
response_shape)
if args.testrespfile is not None:
test_responses = unravel_2D(
response_scaler.transform(ravel_2D(test_responses)),
test_responses_shape)
test_responses = np.expand_dims(test_responses, axis=1)
factor = args.m
x_context = np.zeros([covariates.shape[0], factor, covariates.shape[1]],
dtype=np.float32)
y_context = np.zeros([
responses.shape[0], factor, responses.shape[1], responses.shape[2],
responses.shape[3]
],
dtype=np.float32)
x_all = np.zeros([covariates.shape[0], factor, covariates.shape[1]],
dtype=np.float32)
x_context_test = np.zeros(
[test_covariates.shape[0], factor, test_covariates.shape[1]],
dtype=np.float32)
y_context_test = np.zeros([
test_covariates.shape[0], factor, responses.shape[1],
responses.shape[2], responses.shape[3]
],
dtype=np.float32)
print('Estimating the fixed-effects ...')
for i in range(factor):
x_context[:, i, :] = covariates[:, :]
x_context_test[:, i, :] = test_covariates[:, :]
idx = np.random.randint(0, covariates.shape[0], covariates.shape[0])
if args.estimator == 'ST':
for j in range(responses.shape[1]):
for k in range(responses.shape[2]):
for l in range(responses.shape[3]):
reg = LinearRegression()
reg.fit(x_context[idx, i, :], responses[idx, j, k, l])
y_context[:, i, j, k, l] = reg.predict(x_context[:,
i, :])
y_context_test[:, i, j, k,
l] = reg.predict(x_context_test[:,
i, :])
elif args.estimator == 'MT':
reg = MultiTaskLasso(alpha=0.1)
reg.fit(
x_context[idx, i, :],
np.reshape(responses[idx, :, :, :],
[covariates.shape[0],
np.prod(responses.shape[1:])]))
y_context[:, i, :, :, :] = np.reshape(
reg.predict(x_context[:, i, :]), [
x_context.shape[0], responses.shape[1], responses.shape[2],
responses.shape[3]
])
y_context_test[:, i, :, :, :] = np.reshape(
reg.predict(x_context_test[:, i, :]), [
x_context_test.shape[0], responses.shape[1],
responses.shape[2], responses.shape[3]
])
print('Fixed-effect %d of %d is computed!' % (i + 1, factor))
x_all = x_context
responses = np.expand_dims(responses, axis=1).repeat(factor, axis=1)
################################## TRAINING #################################
encoder = Encoder(x_context, y_context, args).to(args.device)
args.cnn_feature_num = encoder.cnn_feature_num
decoder = Decoder(x_context, y_context, args).to(args.device)
model = NP(encoder, decoder, args).to(args.device)
print('Estimating the Random-effect ...')
k = 1
epochs = [
int(args.epochs / 4),
int(args.epochs / 2),
int(args.epochs / 5),
int(args.epochs - args.epochs / 4 - args.epochs / 2 - args.epochs / 5)
]
mini_batch_num = args.batchnum
batch_size = int(x_context.shape[0] / mini_batch_num)
model.train()
for e in range(len(epochs)):
optimizer = optim.Adam(model.parameters(), lr=10**(-e - 2))
for j in range(epochs[e]):
train_loss = 0
rand_idx = np.random.permutation(x_context.shape[0])
for i in range(mini_batch_num):
optimizer.zero_grad()
idx = rand_idx[i * batch_size:(i + 1) * batch_size]
y_hat, z_all, z_context, dummy = model(
torch.tensor(x_context[idx, :, :], device=args.device),
torch.tensor(y_context[idx, :, :, :, :],
device=args.device),
torch.tensor(x_all[idx, :, :], device=args.device),
torch.tensor(responses[idx, :, :, :, :],
device=args.device))
loss = np_loss(
y_hat,
torch.tensor(responses[idx, :, :, :, :],
device=args.device), z_all, z_context)
loss.backward()
train_loss += loss.item()
optimizer.step()
print('Epoch: %d, Loss:%f, Average Loss:%f' %
(k, train_loss, train_loss / responses.shape[0]))
k += 1
################################## Evaluation #################################
print('Predicting on Test Data ...')
model.eval()
model.apply(apply_dropout_test)
with torch.no_grad():
y_hat, z_all, z_context, y_sigma = model(
torch.tensor(x_context_test, device=args.device),
torch.tensor(y_context_test, device=args.device),
n=15)
if args.testrespfile is not None:
test_loss = np_loss(y_hat[0:test_responses_shape[0], :],
torch.tensor(test_responses, device=args.device),
z_all, z_context).item()
print('Average Test Loss:%f' % (test_loss / test_responses_shape[0]))
RMSE = np.sqrt(
np.mean((test_responses -
y_hat[0:test_responses_shape[0], :].cpu().numpy())**2,
axis=0)).squeeze() * mask
SMSE = RMSE**2 / np.var(test_responses, axis=0).squeeze()
Rho, pRho = compute_pearsonr(
test_responses.squeeze(),
y_hat[0:test_responses_shape[0], :].cpu().numpy().squeeze())
EXPV = explained_var(
test_responses.squeeze(),
y_hat[0:test_responses_shape[0], :].cpu().numpy().squeeze()) * mask
MSLL = compute_MSLL(
test_responses.squeeze(),
y_hat[0:test_responses_shape[0], :].cpu().numpy().squeeze(),
y_sigma[0:test_responses_shape[0], :].cpu().numpy().squeeze()**2,
train_mean=test_responses.mean(0),
train_var=test_responses.var(0)).squeeze() * mask
NPMs = (test_responses -
y_hat[0:test_responses_shape[0], :].cpu().numpy()) / (
y_sigma[0:test_responses_shape[0], :].cpu().numpy())
NPMs = NPMs.squeeze()
NPMs = NPMs * mask
NPMs = np.nan_to_num(NPMs)
temp = NPMs.reshape(
[NPMs.shape[0], NPMs.shape[1] * NPMs.shape[2] * NPMs.shape[3]])
EVD_params = extreme_value_prob_fit(temp, 0.01)
abnormal_probs = extreme_value_prob(EVD_params, temp, 0.01)
############################## SAVING RESULTS #################################
print('Saving Results to: %s' % (args.outdir))
exfile = args.respfile
y_hat = y_hat.squeeze().cpu().numpy()
y_hat = response_scaler.inverse_transform(ravel_2D(y_hat))
y_hat = y_hat[:, mask.flatten()]
fileio.save(y_hat.T,
args.outdir + '/yhat.nii.gz',
example=exfile,
mask=mask)
ys2 = y_sigma.squeeze().cpu().numpy()
ys2 = ravel_2D(ys2) * (response_scaler.data_max_ -
response_scaler.data_min_)
ys2 = ys2**2
ys2 = ys2[:, mask.flatten()]
fileio.save(ys2.T, args.outdir + '/ys2.nii.gz', example=exfile, mask=mask)
if args.testrespfile is not None:
NPMs = ravel_2D(NPMs)[:, mask.flatten()]
fileio.save(NPMs.T,
args.outdir + '/Z.nii.gz',
example=exfile,
mask=mask)
fileio.save(Rho.flatten()[mask.flatten()],
args.outdir + '/Rho.nii.gz',
example=exfile,
mask=mask)
fileio.save(pRho.flatten()[mask.flatten()],
args.outdir + '/pRho.nii.gz',
example=exfile,
mask=mask)
fileio.save(RMSE.flatten()[mask.flatten()],
args.outdir + '/rmse.nii.gz',
example=exfile,
mask=mask)
fileio.save(SMSE.flatten()[mask.flatten()],
args.outdir + '/smse.nii.gz',
example=exfile,
mask=mask)
fileio.save(EXPV.flatten()[mask.flatten()],
args.outdir + '/expv.nii.gz',
example=exfile,
mask=mask)
fileio.save(MSLL.flatten()[mask.flatten()],
args.outdir + '/msll.nii.gz',
example=exfile,
mask=mask)
with open(args.outdir + 'model.pkl', 'wb') as handle:
pickle.dump(
{
'model': model,
'covariates_scaler': covariates_scaler,
'response_scaler': response_scaler,
'EVD_params': EVD_params,
'abnormal_probs': abnormal_probs
},
handle,
protocol=pickle.HIGHEST_PROTOCOL)
###############################################################################
print('DONE!')
def collect_nm(processing_dir, collect=False, binary=False):
"""This function checks and collects all batches.
** Input:
* processing_dir -> Full path to the processing directory
* collect -> If True data is checked for failed batches
and collected; if False data is just checked
** Output:
* Text files containing all results accross all batches the combined
output
written by (primarily) T Wolfers, (adapted) SM Kia
"""
# import of necessary modules
import os
import sys
import glob
import numpy as np
import pandas as pd
try:
import nispat.fileio as fileio
except ImportError:
pass
path = os.path.abspath(os.path.dirname(__file__))
if path not in sys.path:
sys.path.append(path)
del path
import fileio
if binary:
file_extentions = '.pkl'
else:
file_extentions = '.txt'
# detect number of subjects, batches, hyperparameters and CV
file_example = glob.glob(processing_dir + 'batch_1/' + 'yhat' +
file_extentions)
if binary is False:
file_example = fileio.load(file_example[0])
else:
file_example = pd.read_pickle(file_example[0])
numsubjects = file_example.shape[0]
batch_size = file_example.shape[1]
all_Hyptxt = glob.glob(processing_dir + 'batch_*/' + 'Hyp*')
if all_Hyptxt != []:
first_Hyptxt = fileio.load(all_Hyptxt[0])
first_Hyptxt = first_Hyptxt.transpose()
nHyp = len(first_Hyptxt)
dir_first_Hyptxt = os.path.dirname(all_Hyptxt[0])
all_crossval = glob.glob(dir_first_Hyptxt + '/' + 'Hyp*')
n_crossval = len(all_crossval)
# artificially creates files for batches that were not executed
count = 0
batch_fail = []
for batch in glob.glob(processing_dir + 'batch_*/'):
filepath = glob.glob(batch + 'yhat*')
if filepath == []:
count = count + 1
batch1 = glob.glob(batch + '/*.sh')
print(batch1)
batch_fail.append(batch1)
if collect is True:
pRho = np.ones(batch_size)
pRho = pRho.transpose()
pRho = pd.Series(pRho)
fileio.save(pRho, batch + 'pRho' + file_extentions)
Rho = np.zeros(batch_size)
Rho = Rho.transpose()
Rho = pd.Series(Rho)
fileio.save(Rho, batch + 'Rho' + file_extentions)
rmse = np.zeros(batch_size)
rmse = rmse.transpose()
rmse = pd.Series(rmse)
fileio.save(rmse, batch + 'rmse' + file_extentions)
smse = np.zeros(batch_size)
smse = smse.transpose()
smse = pd.Series(smse)
fileio.save(smse, batch + 'smse' + file_extentions)
expv = np.zeros(batch_size)
expv = expv.transpose()
expv = pd.Series(expv)
fileio.save(expv, batch + 'expv' + file_extentions)
msll = np.zeros(batch_size)
msll = msll.transpose()
msll = pd.Series(msll)
fileio.save(msll, batch + 'msll' + file_extentions)
yhat = np.zeros([batch_size, numsubjects])
yhat = pd.DataFrame(yhat)
fileio.save(yhat, batch + 'yhat' + file_extentions)
ys2 = np.zeros([batch_size, numsubjects])
ys2 = pd.DataFrame(ys2)
fileio.save(ys2, batch + 'ys2' + file_extentions)
Z = np.zeros([batch_size, numsubjects])
Z = pd.DataFrame(Z)
fileio.save(Z, batch + 'Z' + file_extentions)
for n in range(1, n_crossval + 1):
hyp = np.zeros([batch_size, nHyp])
hyp = pd.DataFrame(hyp)
fileio.save(hyp, batch + 'hyp' + file_extentions)
else: # if more than 10% of yhat is nan then consider the batch as a failed batch
yhat = fileio.load(filepath[0])
if np.count_nonzero(~np.isnan(yhat)) / (np.prod(yhat.shape)) < 0.9:
count = count + 1
batch1 = glob.glob(batch + '/*.sh')
print('More than 10% nans in ' + batch1[0])
batch_fail.append(batch1)
# list batches that were not executed
print('Number of batches that failed:' + str(count))
batch_fail_df = pd.DataFrame(batch_fail)
if file_extentions == '.txt':
fileio.save_pd(batch_fail_df,
processing_dir + 'failed_batches' + file_extentions)
else:
fileio.save(batch_fail_df,
processing_dir + 'failed_batches' + file_extentions)
# combines all output files across batches
if collect is True:
pRho_filenames = glob.glob(processing_dir + 'batch_*/' + 'pRho*')
if pRho_filenames:
pRho_filenames = fileio.sort_nicely(pRho_filenames)
pRho_dfs = []
for pRho_filename in pRho_filenames:
pRho_dfs.append(pd.DataFrame(fileio.load(pRho_filename)))
pRho_combined = pd.concat(pRho_dfs, ignore_index=True)
fileio.save(pRho_combined,
processing_dir + 'pRho' + file_extentions)
Rho_filenames = glob.glob(processing_dir + 'batch_*/' + 'Rho*')
if pRho_filenames:
Rho_filenames = fileio.sort_nicely(Rho_filenames)
Rho_dfs = []
for Rho_filename in Rho_filenames:
Rho_dfs.append(pd.DataFrame(fileio.load(Rho_filename)))
Rho_combined = pd.concat(Rho_dfs, ignore_index=True)
fileio.save(Rho_combined, processing_dir + 'Rho' + file_extentions)
Z_filenames = glob.glob(processing_dir + 'batch_*/' + 'Z*')
if Z_filenames:
Z_filenames = fileio.sort_nicely(Z_filenames)
Z_dfs = []
for Z_filename in Z_filenames:
Z_dfs.append(pd.DataFrame(fileio.load(Z_filename)))
Z_combined = pd.concat(Z_dfs, ignore_index=True)
fileio.save(Z_combined, processing_dir + 'Z' + file_extentions)
yhat_filenames = glob.glob(processing_dir + 'batch_*/' + 'yhat*')
if yhat_filenames:
yhat_filenames = fileio.sort_nicely(yhat_filenames)
yhat_dfs = []
for yhat_filename in yhat_filenames:
yhat_dfs.append(pd.DataFrame(fileio.load(yhat_filename)))
yhat_combined = pd.concat(yhat_dfs, ignore_index=True)
fileio.save(yhat_combined,
processing_dir + 'yhat' + file_extentions)
ys2_filenames = glob.glob(processing_dir + 'batch_*/' + 'ys2*')
if ys2_filenames:
ys2_filenames = fileio.sort_nicely(ys2_filenames)
ys2_dfs = []
for ys2_filename in ys2_filenames:
ys2_dfs.append(pd.DataFrame(fileio.load(ys2_filename)))
ys2_combined = pd.concat(ys2_dfs, ignore_index=True)
fileio.save(ys2_combined, processing_dir + 'ys2' + file_extentions)
rmse_filenames = glob.glob(processing_dir + 'batch_*/' + 'rmse*')
if rmse_filenames:
rmse_filenames = fileio.sort_nicely(rmse_filenames)
rmse_dfs = []
for rmse_filename in rmse_filenames:
rmse_dfs.append(pd.DataFrame(fileio.load(rmse_filename)))
rmse_combined = pd.concat(rmse_dfs, ignore_index=True)
fileio.save(rmse_combined,
processing_dir + 'rmse' + file_extentions)
smse_filenames = glob.glob(processing_dir + 'batch_*/' + 'smse*')
if rmse_filenames:
smse_filenames = fileio.sort_nicely(smse_filenames)
smse_dfs = []
for smse_filename in smse_filenames:
smse_dfs.append(pd.DataFrame(fileio.load(smse_filename)))
smse_combined = pd.concat(smse_dfs, ignore_index=True)
fileio.save(smse_combined,
processing_dir + 'smse' + file_extentions)
expv_filenames = glob.glob(processing_dir + 'batch_*/' + 'expv*')
if expv_filenames:
expv_filenames = fileio.sort_nicely(expv_filenames)
expv_dfs = []
for expv_filename in expv_filenames:
expv_dfs.append(pd.DataFrame(fileio.load(expv_filename)))
expv_combined = pd.concat(expv_dfs, ignore_index=True)
fileio.save(expv_combined,
processing_dir + 'expv' + file_extentions)
msll_filenames = glob.glob(processing_dir + 'batch_*/' + 'msll*')
if msll_filenames:
msll_filenames = fileio.sort_nicely(msll_filenames)
msll_dfs = []
for msll_filename in msll_filenames:
msll_dfs.append(pd.DataFrame(fileio.load(msll_filename)))
msll_combined = pd.concat(msll_dfs, ignore_index=True)
fileio.save(msll_combined,
processing_dir + 'msll' + file_extentions)
for n in range(1, n_crossval + 1):
Hyp_filenames = glob.glob(processing_dir + 'batch_*/' + 'Hyp_' +
str(n) + '.*')
if Hyp_filenames:
Hyp_filenames = fileio.sort_nicely(Hyp_filenames)
Hyp_dfs = []
for Hyp_filename in Hyp_filenames:
Hyp_dfs.append(pd.DataFrame(fileio.load(Hyp_filename)))
Hyp_combined = pd.concat(Hyp_dfs, ignore_index=True)
fileio.save(Hyp_combined,
processing_dir + 'Hyp_' + str(n) + file_extentions)
def collect_nm(processing_dir,
job_name,
func='estimate',
collect=False,
binary=False,
batch_size=None,
outputsuffix=''):
"""This function checks and collects all batches.
** Input:
* processing_dir -> Full path to the processing directory
* collect -> If True data is checked for failed batches
and collected; if False data is just checked
** Output:
* Text files containing all results accross all batches the combined
output
written by (primarily) T Wolfers, (adapted) SM Kia
"""
if binary:
file_extentions = '.pkl'
else:
file_extentions = '.txt'
# detect number of subjects, batches, hyperparameters and CV
batches = glob.glob(processing_dir + 'batch_*/')
file_example = []
for batch in batches:
if file_example == []:
file_example = glob.glob(batch + 'yhat' + outputsuffix +
file_extentions)
else:
break
if binary is False:
file_example = fileio.load(file_example[0])
else:
file_example = pd.read_pickle(file_example[0])
numsubjects = file_example.shape[0]
batch_size = file_example.shape[1]
# artificially creates files for batches that were not executed
count = 0
batch_fail = []
batch_dirs = glob.glob(processing_dir + 'batch_*/')
batch_dirs = fileio.sort_nicely(batch_dirs)
for batch in batch_dirs:
filepath = glob.glob(batch + 'yhat' + outputsuffix + '*')
if filepath == []:
count = count + 1
batch1 = glob.glob(batch + '/' + job_name + '*.sh')
print(batch1)
batch_fail.append(batch1)
if collect is True:
pRho = np.ones(batch_size)
pRho = pRho.transpose()
pRho = pd.Series(pRho)
fileio.save(pRho,
batch + 'pRho' + outputsuffix + file_extentions)
Rho = np.zeros(batch_size)
Rho = Rho.transpose()
Rho = pd.Series(Rho)
fileio.save(Rho,
batch + 'Rho' + outputsuffix + file_extentions)
rmse = np.zeros(batch_size)
rmse = rmse.transpose()
rmse = pd.Series(rmse)
fileio.save(rmse,
batch + 'RMSE' + outputsuffix + file_extentions)
smse = np.zeros(batch_size)
smse = smse.transpose()
smse = pd.Series(smse)
fileio.save(smse,
batch + 'SMSE' + outputsuffix + file_extentions)
expv = np.zeros(batch_size)
expv = expv.transpose()
expv = pd.Series(expv)
fileio.save(expv,
batch + 'EXPV' + outputsuffix + file_extentions)
msll = np.zeros(batch_size)
msll = msll.transpose()
msll = pd.Series(msll)
fileio.save(msll,
batch + 'MSLL' + outputsuffix + file_extentions)
yhat = np.zeros([numsubjects, batch_size])
yhat = pd.DataFrame(yhat)
fileio.save(yhat,
batch + 'yhat' + outputsuffix + file_extentions)
ys2 = np.zeros([numsubjects, batch_size])
ys2 = pd.DataFrame(ys2)
fileio.save(ys2,
batch + 'ys2' + outputsuffix + file_extentions)
Z = np.zeros([numsubjects, batch_size])
Z = pd.DataFrame(Z)
fileio.save(Z, batch + 'Z' + outputsuffix + file_extentions)
if not os.path.isdir(batch + 'Models'):
os.mkdir('Models')
else: # if more than 10% of yhat is nan then consider the batch as a failed batch
yhat = fileio.load(filepath[0])
if np.count_nonzero(~np.isnan(yhat)) / (np.prod(yhat.shape)) < 0.9:
count = count + 1
batch1 = glob.glob(batch + '/' + job_name + '*.sh')
print('More than 10% nans in ' + batch1[0])
batch_fail.append(batch1)
# list batches that were not executed
print('Number of batches that failed:' + str(count))
batch_fail_df = pd.DataFrame(batch_fail)
if file_extentions == '.txt':
fileio.save_pd(batch_fail_df,
processing_dir + 'failed_batches' + file_extentions)
else:
fileio.save(batch_fail_df,
processing_dir + 'failed_batches' + file_extentions)
# combines all output files across batches
if collect is True:
pRho_filenames = glob.glob(processing_dir + 'batch_*/' + 'pRho' +
outputsuffix + '*')
if pRho_filenames:
pRho_filenames = fileio.sort_nicely(pRho_filenames)
pRho_dfs = []
for pRho_filename in pRho_filenames:
pRho_dfs.append(pd.DataFrame(fileio.load(pRho_filename)))
pRho_dfs = pd.concat(pRho_dfs, ignore_index=True, axis=0)
fileio.save(
pRho_dfs,
processing_dir + 'pRho' + outputsuffix + file_extentions)
del pRho_dfs
Rho_filenames = glob.glob(processing_dir + 'batch_*/' + 'Rho' +
outputsuffix + '*')
if pRho_filenames:
Rho_filenames = fileio.sort_nicely(Rho_filenames)
Rho_dfs = []
for Rho_filename in Rho_filenames:
Rho_dfs.append(pd.DataFrame(fileio.load(Rho_filename)))
Rho_dfs = pd.concat(Rho_dfs, ignore_index=True, axis=0)
fileio.save(
Rho_dfs,
processing_dir + 'Rho' + outputsuffix + file_extentions)
del Rho_dfs
Z_filenames = glob.glob(processing_dir + 'batch_*/' + 'Z' +
outputsuffix + '*')
if Z_filenames:
Z_filenames = fileio.sort_nicely(Z_filenames)
Z_dfs = []
for Z_filename in Z_filenames:
Z_dfs.append(pd.DataFrame(fileio.load(Z_filename)))
Z_dfs = pd.concat(Z_dfs, ignore_index=True, axis=1)
fileio.save(Z_dfs,
processing_dir + 'Z' + outputsuffix + file_extentions)
del Z_dfs
yhat_filenames = glob.glob(processing_dir + 'batch_*/' + 'yhat' +
outputsuffix + '*')
if yhat_filenames:
yhat_filenames = fileio.sort_nicely(yhat_filenames)
yhat_dfs = []
for yhat_filename in yhat_filenames:
yhat_dfs.append(pd.DataFrame(fileio.load(yhat_filename)))
yhat_dfs = pd.concat(yhat_dfs, ignore_index=True, axis=1)
fileio.save(
yhat_dfs,
processing_dir + 'yhat' + outputsuffix + file_extentions)
del yhat_dfs
ys2_filenames = glob.glob(processing_dir + 'batch_*/' + 'ys2' +
outputsuffix + '*')
if ys2_filenames:
ys2_filenames = fileio.sort_nicely(ys2_filenames)
ys2_dfs = []
for ys2_filename in ys2_filenames:
ys2_dfs.append(pd.DataFrame(fileio.load(ys2_filename)))
ys2_dfs = pd.concat(ys2_dfs, ignore_index=True, axis=1)
fileio.save(
ys2_dfs,
processing_dir + 'ys2' + outputsuffix + file_extentions)
del ys2_dfs
rmse_filenames = glob.glob(processing_dir + 'batch_*/' + 'RMSE' +
outputsuffix + '*')
if rmse_filenames:
rmse_filenames = fileio.sort_nicely(rmse_filenames)
rmse_dfs = []
for rmse_filename in rmse_filenames:
rmse_dfs.append(pd.DataFrame(fileio.load(rmse_filename)))
rmse_dfs = pd.concat(rmse_dfs, ignore_index=True, axis=0)
fileio.save(
rmse_dfs,
processing_dir + 'RMSE' + outputsuffix + file_extentions)
del rmse_dfs
smse_filenames = glob.glob(processing_dir + 'batch_*/' + 'SMSE' +
outputsuffix + '*')
if rmse_filenames:
smse_filenames = fileio.sort_nicely(smse_filenames)
smse_dfs = []
for smse_filename in smse_filenames:
smse_dfs.append(pd.DataFrame(fileio.load(smse_filename)))
smse_dfs = pd.concat(smse_dfs, ignore_index=True, axis=0)
fileio.save(
smse_dfs,
processing_dir + 'SMSE' + outputsuffix + file_extentions)
del smse_dfs
expv_filenames = glob.glob(processing_dir + 'batch_*/' + 'EXPV' +
outputsuffix + '*')
if expv_filenames:
expv_filenames = fileio.sort_nicely(expv_filenames)
expv_dfs = []
for expv_filename in expv_filenames:
expv_dfs.append(pd.DataFrame(fileio.load(expv_filename)))
expv_dfs = pd.concat(expv_dfs, ignore_index=True, axis=0)
fileio.save(
expv_dfs,
processing_dir + 'EXPV' + outputsuffix + file_extentions)
del expv_dfs
msll_filenames = glob.glob(processing_dir + 'batch_*/' + 'MSLL' +
outputsuffix + '*')
if msll_filenames:
msll_filenames = fileio.sort_nicely(msll_filenames)
msll_dfs = []
for msll_filename in msll_filenames:
msll_dfs.append(pd.DataFrame(fileio.load(msll_filename)))
msll_dfs = pd.concat(msll_dfs, ignore_index=True, axis=0)
fileio.save(
msll_dfs,
processing_dir + 'MSLL' + outputsuffix + file_extentions)
del msll_dfs
if func != 'predict':
if not os.path.isdir(processing_dir + 'Models') and \
os.path.exists(os.path.join(batches[0], 'Models')):
os.mkdir(processing_dir + 'Models')
meta_filenames = glob.glob(processing_dir + 'batch_*/Models/' +
'meta_data.md')
mY = []
sY = []
mX = []
sX = []
if meta_filenames:
meta_filenames = fileio.sort_nicely(meta_filenames)
with open(meta_filenames[0], 'rb') as file:
meta_data = pickle.load(file)
if meta_data['standardize']:
for meta_filename in meta_filenames:
mY.append(meta_data['mean_resp'])
sY.append(meta_data['std_resp'])
mX.append(meta_data['mean_cov'])
sX.append(meta_data['std_cov'])
meta_data['mean_resp'] = np.stack(mY)
meta_data['std_resp'] = np.stack(sY)
meta_data['mean_cov'] = np.stack(mX)
meta_data['std_cov'] = np.stack(sX)
with open(
os.path.join(processing_dir, 'Models', 'meta_data.md'),
'wb') as file:
pickle.dump(meta_data, file)
batch_dirs = glob.glob(processing_dir + 'batch_*/')
if batch_dirs:
batch_dirs = fileio.sort_nicely(batch_dirs)
for b, batch_dir in enumerate(batch_dirs):
src_files = glob.glob(batch_dir + 'Models/*.pkl')
src_files = fileio.sort_nicely(src_files)
for f, full_file_name in enumerate(src_files):
if os.path.isfile(full_file_name):
file_name = full_file_name.split('/')[-1]
n = file_name.split('_')
n[-1] = str(b * batch_size + f) + '.pkl'
n = '_'.join(n)
shutil.copy(full_file_name,
processing_dir + 'Models/' + n)
if not batch_fail:
return 1
else:
return 0