def stimuli_recon(prf_dir, db_dir, subj_id, roi):
"""Reconstruct stimulus based on pRF model."""
# load fmri response
vxl_idx, train_fmri_ts, val_fmri_ts = dataio.load_vim1_fmri(db_dir,
subj_id,
roi=roi)
del train_fmri_ts
print 'Voxel number: %s' % (len(vxl_idx))
# load model parameters
roi_dir = os.path.join(prf_dir, roi)
val_corr = np.load(os.path.join(roi_dir, 'reg_sel_model_corr.npy'))
filters = np.load(os.path.join(roi_dir, 'filters.npy'))
recon_imgs = np.zeros((val_fmri_ts.shape[1], 500, 500))
# fMRI data z-score
print 'fmri data temporal z-score'
m = np.mean(val_fmri_ts, axis=1, keepdims=True)
s = np.std(val_fmri_ts, axis=1, keepdims=True)
val_fmri_ts = (val_fmri_ts - m) / (1e-10 + s)
# select significant predicted voxels
sel_vxls = np.nonzero(val_corr >= 0.24)[0]
for i in range(val_fmri_ts.shape[1]):
print 'Reconstruct stimilus %s' % (i + 1)
tmp = np.zeros((500, 500))
for j in sel_vxls:
tmp += val_fmri_ts[int(j), int(i)] * filters[j]
recon_imgs[i] = tmp
np.save(os.path.join(roi_dir, 'recon_img.npy'), recon_imgs)
def null_distribution_prf_tunning(feat_dir, prf_dir, db_dir, subj_id, roi):
"""Generate Null distribution of pRF model tunning using validation data."""
# load fmri response
vxl_idx, train_fmri_ts, val_fmri_ts = dataio.load_vim1_fmri(db_dir,
subj_id,
roi=roi)
del train_fmri_ts
print 'Voxel number: %s' % (len(vxl_idx))
# load candidate models
val_models = np.load(os.path.join(feat_dir, 'val_candidate_model.npy'),
mmap_mode='r')
# output directory config
roi_dir = os.path.join(prf_dir, roi)
# load selected model parameters
paras = np.load(os.path.join(roi_dir, 'reg_sel_paras.npy'))
sel_model = np.load(os.path.join(roi_dir, 'reg_sel_model.npy'))
null_corr = np.zeros((paras.shape[0], 1000))
for i in range(paras.shape[0]):
print 'Voxel %s' % (i)
# load features
feats = np.array(val_models[int(sel_model[i]), ...]).astype(np.float64)
feats = zscore(feats.T).T
pred = np.dot(feats, paras[i])
for j in range(1000):
shuffled_val_ts = np.random.permutation(val_fmri_ts[i])
null_corr[i, j] = np.corrcoef(pred, shuffled_val_ts)[0, 1]
np.save(os.path.join(roi_dir, 'random_corr.npy'), null_corr)
def filter_recon(prf_dir, db_dir, subj_id, roi):
"""Reconstruct filter map of each voxel based on selected model."""
# load fmri response
vxl_idx, train_fmri_ts, val_fmri_ts = dataio.load_vim1_fmri(db_dir,
subj_id,
roi=roi)
del train_fmri_ts
del val_fmri_ts
print 'Voxel number: %s' % (len(vxl_idx))
# output config
roi_dir = os.path.join(prf_dir, roi)
# pRF estimate
sel_models = np.load(os.path.join(roi_dir, 'reg_sel_model.npy'))
sel_paras = np.load(os.path.join(roi_dir, 'reg_sel_paras.npy'))
sel_model_corr = np.load(os.path.join(roi_dir, 'reg_sel_model_corr.npy'))
filters = np.zeros((sel_models.shape[0], 500, 500))
fig_dir = os.path.join(roi_dir, 'filters')
check_path(fig_dir)
thr = 0.24
# gabor bank generation
gwt = bob.ip.gabor.Transform(number_of_scales=9)
gwt.generate_wavelets(500, 500)
spatial_gabors = np.zeros((72, 500, 500))
for i in range(72):
w = bob.ip.gabor.Wavelet(resolution=(500, 500),
frequency=gwt.wavelet_frequencies[i])
sw = bob.sp.ifft(w.wavelet.astype(np.complex128))
spatial_gabors[i, ...] = np.roll(np.roll(np.real(sw), 250, 0), 250, 1)
for i in range(sel_models.shape[0]):
if sel_model_corr[i] < thr:
continue
print 'Voxel %s, Val Corr %s' % (i, sel_model_corr[i])
model_idx = int(sel_models[i])
# get gaussian pooling field parameters
si = model_idx / 2500
xi = (model_idx % 2500) / 50
yi = (model_idx % 2500) % 50
x0 = np.arange(5, 500, 10)[xi]
y0 = np.arange(5, 500, 10)[yi]
sigma = [1] + [n * 5 for n in range(1, 13)] + [70, 80, 90, 100]
s = sigma[si]
print 'center: %s, %s, sigma: %s' % (y0, x0, s)
kernel = make_2d_gaussian(500, s, center=(x0, y0))
kpos = np.nonzero(kernel > 0.00000001)
paras = sel_paras[i]
tmp_file = os.path.join(fig_dir, 'tmp_kernel.npy')
tmp_filter = np.memmap(tmp_file,
dtype='float64',
mode='w+',
shape=(72, 500, 500))
Parallel(n_jobs=25)(delayed(filter_pro)(tmp_filter, paras, kernel,
kpos, spatial_gabors, gwt_idx)
for gwt_idx in range(72))
tmp_filter = np.array(tmp_filter)
filters[i] = tmp_filter.sum(axis=0)
os.system('rm %s' % (tmp_file))
im_file = os.path.join(fig_dir,
'Voxel_%s_%s.png' % (i + 1, vxl_idx[i]))
vutil.save_imshow(filters[i], im_file)
np.save(os.path.join(roi_dir, 'filters.npy'), filters)
def gabor_contribution2prf(feat_dir, prf_dir, db_dir, subj_id, roi):
"""Calculate tunning contribution of each gabor sub-banks."""
# load fmri response
vxl_idx, train_fmri_ts, val_fmri_ts = dataio.load_vim1_fmri(db_dir,
subj_id,
roi=roi)
del train_fmri_ts
print 'Voxel number: %s' % (len(vxl_idx))
# load candidate models
val_models = np.load(os.path.join(feat_dir, 'val_candidate_model.npy'),
mmap_mode='r')
# load selected model parameters
roi_dir = os.path.join(prf_dir, roi)
paras = np.load(os.path.join(roi_dir, 'reg_sel_paras.npy'))
sel_model = np.load(os.path.join(roi_dir, 'reg_sel_model.npy'))
gabor_corr = np.zeros((paras.shape[0], 9))
for i in range(paras.shape[0]):
print 'Voxel %s' % (i)
# load features
feats = np.array(val_models[int(sel_model[i]), ...]).astype(np.float64)
feats = zscore(feats.T).T
for j in range(9):
pred = np.dot(feats[:, (j * 8):(j * 8 + 8)],
paras[i, (j * 8):(j * 8 + 8)])
gabor_corr[i, j] = np.corrcoef(pred, val_fmri_ts[i])[0, 1]
np.save(os.path.join(roi_dir, 'gabor_contributes.npy'), gabor_corr)
def prf_selection(feat_dir, prf_dir, db_dir, subj_id, roi):
"""Select best model for each voxel and validating."""
# load fmri response
vxl_idx, train_fmri_ts, val_fmri_ts = dataio.load_vim1_fmri(db_dir,
subj_id,
roi=roi)
del train_fmri_ts
print 'Voxel number: %s' % (len(vxl_idx))
# load candidate models
val_models = np.load(os.path.join(feat_dir, 'val_candidate_model.npy'),
mmap_mode='r')
# output directory config
roi_dir = os.path.join(prf_dir, roi)
# load candidate model parameters
paras = np.load(os.path.join(roi_dir, 'reg_paras.npy'))
mcorr = np.load(os.path.join(roi_dir, 'reg_model_corr.npy'))
alphas = np.load(os.path.join(roi_dir, 'reg_alphas.npy'))
sel_paras = np.zeros((mcorr.shape[1], 72))
sel_model = np.zeros(mcorr.shape[1])
sel_model_corr = np.zeros(mcorr.shape[1])
for i in range(mcorr.shape[1]):
maxi = np.argmax(np.nan_to_num(mcorr[:, i]))
print 'Voxel %s - Max corr %s - Model %s' % (i, mcorr[maxi, i], maxi)
print 'Alpha : %s' % (alphas[maxi, i])
sel_paras[i] = paras[maxi, i]
sel_model[i] = maxi
feats = np.array(val_models[maxi, ...]).astype(np.float64)
feats = zscore(feats.T).T
pred = np.dot(feats, sel_paras[i])
sel_model_corr[i] = np.corrcoef(pred, val_fmri_ts[i])[0, 1]
print 'Val Corr : %s' % (sel_model_corr[i])
np.save(os.path.join(roi_dir, 'reg_sel_paras.npy'), sel_paras)
np.save(os.path.join(roi_dir, 'reg_sel_model.npy'), sel_model)
np.save(os.path.join(roi_dir, 'reg_sel_model_corr.npy'), sel_model_corr)
def get_vxl_idx(prf_dir, db_dir, subj_id, roi):
"""Get voxel index in specific ROI"""
# load fmri response
vxl_idx, train_fmri_ts, val_fmri_ts = dataio.load_vim1_fmri(db_dir,
subj_id,
roi=roi)
print 'Voxel number: %s' % (len(vxl_idx))
roi_dir = os.path.join(prf_dir, roi)
check_path(roi_dir)
np.save(os.path.join(roi_dir, 'vxl_idx.npy'), vxl_idx)
def prf_recon(prf_dir, db_dir, subj_id, roi):
"""Reconstruct pRF based on selected model."""
# load fmri response
vxl_idx, train_fmri_ts, val_fmri_ts = dataio.load_vim1_fmri(db_dir,
subj_id,
roi=roi)
del train_fmri_ts
del val_fmri_ts
print 'Voxel number: %s' % (len(vxl_idx))
# output directory config
roi_dir = os.path.join(prf_dir, roi)
# pRF estimate
sel_models = np.load(os.path.join(roi_dir, 'reg_sel_model.npy'))
sel_paras = np.load(os.path.join(roi_dir, 'reg_sel_paras.npy'))
sel_model_corr = np.load(os.path.join(roi_dir, 'reg_sel_model_corr.npy'))
prfs = np.zeros((sel_models.shape[0], 500, 500))
fig_dir = os.path.join(roi_dir, 'figs')
check_path(fig_dir)
for i in range(sel_models.shape[0]):
# get pRF
print 'Voxel %s, Val Corr %s' % (i, sel_model_corr[i])
model_idx = int(sel_models[i])
# get gaussian pooling field parameters
si = model_idx / 2500
xi = (model_idx % 2500) / 50
yi = (model_idx % 2500) % 50
x0 = np.arange(5, 500, 10)[xi]
y0 = np.arange(5, 500, 10)[yi]
sigma = [1] + [n * 5 for n in range(1, 13)] + [70, 80, 90, 100]
s = sigma[si]
kernel = make_2d_gaussian(500, s, center=(x0, y0))
kpos = np.nonzero(kernel)
paras = sel_paras[i]
for f in range(9):
fwt = np.sum(paras[(f * 8):(f * 8 + 8)])
fs = np.sqrt(2)**f * 4
for p in range(kpos[0].shape[0]):
tmp = make_2d_gaussian(500,
fs,
center=(kpos[1][p], kpos[0][p]))
prfs[i] += fwt * kernel[kpos[0][p], kpos[1][p]] * tmp
if sel_model_corr[i] >= 0.24:
prf_file = os.path.join(fig_dir,
'Voxel_%s_%s.png' % (i + 1, vxl_idx[i]))
vutil.save_imshow(prfs[i], prf_file)
np.save(os.path.join(roi_dir, 'prfs.npy'), prfs)
#fpfs = np.zeros((vxl_idx.shape[0], 250, 250))
#biases = np.zeros((vxl_idx.shape[0],))
#for i in range(vxl_idx.shape[0]):
# print 'Voxel %s - %s'%(i, vxl_idx[i])
# vxl_dir = os.path.join(roi_dir, 'voxel_%s'%(vxl_idx[i]), 'refine')
# fpf, b, wt = get_prf_weights(vxl_dir)
# outfile = os.path.join(vxl_dir, 'model_wts')
# np.savez(outfile, fpf=fpf, wt=wt, bias=b)
# fpfs[i, ...] = fpf
# wts[i] = wt
# biases[i] = b
#model_wts_file = os.path.join(roi_dir, 'merged_model_wts')
#np.savez(model_wts_file, fpfs=fpfs, wts=wts, biases=biases)
#-- visual reconstruction using cnn-prf
vxl_idx, train_ts, val_ts = dataio.load_vim1_fmri(db_dir, subj_id, roi=roi)
ts_m = np.mean(val_ts, axis=1, keepdims=True)
ts_s = np.std(val_ts, axis=1, keepdims=True)
val_ts = (val_ts - ts_m) / (ts_s + 1e-5)
# load estimated prf parameters
model_wts = np.load(os.path.join(roi_dir, 'merged_model_wts.npz'))
# load model test result
dl_test_r2 = np.load(os.path.join(roi_dir, 'dl_prf_refine_test_r2.npy'))
# select voxels
thres = 0.1
sel_idx = np.nonzero(dl_test_r2 >= thres)[0]
print 'Select %s voxels for image reconstruction' % (sel_idx.shape[0])
sel_wts = model_wts['wts'][sel_idx]
sel_fpfs = model_wts['fpfs'][sel_idx]
sel_bias = model_wts['biases'][sel_idx]
# get voxel response and reconstruct image
def ridge_regression_model_test(prf_dir, db_dir, subj_id, roi):
"""Test pRF model derived from ridge regression with test dataset."""
# load fmri response
vxl_idx, train_fmri_ts, val_fmri_ts = dataio.load_vim1_fmri(db_dir,
subj_id,
roi=roi)
del train_fmri_ts
print 'Voxel number: %s' % (len(vxl_idx))
# load candidate models
val_models = np.load(os.path.join(db_dir, 'val_candidate_model.npy'),
mmap_mode='r')
# fMRI data z-score
print 'fmri data temporal z-score'
m = np.mean(val_fmri_ts, axis=1, keepdims=True)
s = np.std(val_fmri_ts, axis=1, keepdims=True)
val_fmri_ts = (val_fmri_ts - m) / (1e-5 + s)
# output directory config
roi_dir = os.path.join(prf_dir, roi)
check_path(roi_dir)
# load selected models and the corresponding parameters
val_r2_file = os.path.join(roi_dir, 'reg_val_r2.npy')
val_r2 = np.load(val_r2_file, mmap_mode='r')
paras_file = os.path.join(roi_dir, 'reg_paras.npy')
paras = np.load(paras_file)
alphas_file = os.path.join(roi_dir, 'reg_alphas.npy')
alphas = np.load(alphas_file)
# output var
test_r2 = np.zeros(len(vxl_idx))
prf_pos = np.zeros((len(vxl_idx), 3))
# parameter candidates
alpha_list = np.logspace(-2, 3, 10)
sigma = [2, 4, 8, 16, 32, 60, 70, 80, 90, 100]
for i in range(len(vxl_idx)):
print '----------------'
print 'Voxel %s' % (i)
vxl_r2 = np.nan_to_num(val_r2[i, ...])
sel_mdl_i, sel_alpha_i = np.unravel_index(vxl_r2.argmax(),
vxl_r2.shape)
print 'Select model %s' % (sel_mdl_i)
print 'Select alpha value %s - %s' % (alpha_list[sel_alpha_i],
alphas[i])
# get model position info
xi = (sel_mdl_i % 2500) / 50
yi = (sel_mdl_i % 2500) % 50
x0 = np.arange(2, 250, 5)[xi]
y0 = np.arange(2, 250, 5)[yi]
s = sigma[sel_mdl_i / 2500]
prf_pos[i] = np.array([y0, x0, s])
# compute r^2 using test dataset
test_x = np.array(val_models[sel_mdl_i, ...]).astype(np.float64)
test_x = np.concatenate((np.ones((120, 1)), test_x), axis=1)
val_pred = test_x.dot(paras[i])
ss_tol = np.var(val_fmri_ts[i]) * 120
r2 = 1.0 - np.sum(np.square(val_fmri_ts[i] - val_pred)) / ss_tol
print 'r-square on test dataset: %s' % (r2)
test_r2[i] = r2
# save output
np.save(os.path.join(roi_dir, 'reg_prf_test_r2.npy'), test_r2)
np.save(os.path.join(roi_dir, 'sel_reg_prf_pos.npy'), prf_pos)
def ridge_regression(prf_dir, db_dir, subj_id, roi):
"""pRF model fitting using ridge regression.
90% trainning data used for model tuning, and another 10% data used for
model seletion.
"""
# load fmri response
vxl_idx, train_fmri_ts, val_fmri_ts = dataio.load_vim1_fmri(db_dir,
subj_id,
roi=roi)
del val_fmri_ts
print 'Voxel number: %s' % (len(vxl_idx))
# load candidate models
train_models = np.load(os.path.join(db_dir, 'train_candidate_model.npy'),
mmap_mode='r')
# output directory config
roi_dir = os.path.join(prf_dir, roi)
check_path(roi_dir)
# model seletion and tuning
ALPHA_NUM = 10
paras_file = os.path.join(roi_dir, 'reg_paras.npy')
paras = np.memmap(paras_file,
dtype='float64',
mode='w+',
shape=(len(vxl_idx), 73))
val_r2_file = os.path.join(roi_dir, 'reg_val_r2.npy')
val_r2 = np.memmap(val_r2_file,
dtype='float64',
mode='w+',
shape=(len(vxl_idx), 25000, ALPHA_NUM))
alphas_file = os.path.join(roi_dir, 'reg_alphas.npy')
alphas = np.memmap(alphas_file,
dtype='float64',
mode='w+',
shape=(len(vxl_idx)))
# fMRI data z-score
print 'fmri data temporal z-score'
m = np.mean(train_fmri_ts, axis=1, keepdims=True)
s = np.std(train_fmri_ts, axis=1, keepdims=True)
train_fmri_ts = (train_fmri_ts - m) / (1e-5 + s)
# split training dataset into model tunning set and model selection set
tune_fmri_ts = train_fmri_ts[:, :int(1750 * 0.9)]
sel_fmri_ts = train_fmri_ts[:, int(1750 * 0.9):]
# model fitting
for i in range(len(vxl_idx)):
print '-----------------'
print 'Voxel %s' % (i)
for j in range(25000):
#print 'Model %s'%(j)
# remove models which centered outside the 20 degree of visual angle
xi = (j % 2500) / 50
yi = (j % 2500) % 50
x0 = np.arange(2, 250, 5)[xi]
y0 = np.arange(2, 250, 5)[yi]
d = np.sqrt(np.square(x0 - 125) + np.square(y0 - 125))
if d > 124:
#print 'Model center outside the visual angle'
paras[i, ...] = np.NaN
val_r2[i, j, :] = np.NaN
continue
train_x = np.array(train_models[j, ...]).astype(np.float64)
# split training dataset into model tunning and selection sets
tune_x = train_x[:int(1750 * 0.9), :]
sel_x = train_x[int(1750 * 0.9):, :]
for a in range(ALPHA_NUM):
alpha_list = np.logspace(-2, 3, ALPHA_NUM)
# model fitting
reg = linear_model.Ridge(alpha=alpha_list[a])
reg.fit(tune_x, tune_fmri_ts[i])
val_pred = reg.predict(sel_x)
ss_tol = np.var(sel_fmri_ts[i]) * 175
r2 = 1.0 - np.sum(
np.square(sel_fmri_ts[i] - val_pred)) / ss_tol
val_r2[i, j, a] = r2
# select best model
vxl_r2 = np.nan_to_num(val_r2[i, ...])
sel_mdl_i, sel_alpha_i = np.unravel_index(vxl_r2.argmax(),
vxl_r2.shape)
train_x = np.array(train_models[sel_mdl_i, ...]).astype(np.float64)
# split training dataset into model tunning and selection sets
tune_x = train_x[:int(1750 * 0.9), :]
sel_x = train_x[int(1750 * 0.9):, :]
alpha_list = np.logspace(-2, 3, ALPHA_NUM)
# selected model fitting
reg = linear_model.Ridge(alpha=alpha_list[sel_alpha_i])
reg.fit(tune_x, tune_fmri_ts[i])
val_pred = reg.predict(sel_x)
ss_tol = np.var(sel_fmri_ts[i]) * 175
r2 = 1.0 - np.sum(np.square(sel_fmri_ts[i] - val_pred)) / ss_tol
print 'r-square recal: %s' % (r2)
#print 'r-square cal: %s'%(vxl_r2.max())
paras[i, ...] = np.concatenate((np.array([reg.intercept_]), reg.coef_))
alphas[i] = alpha_list[sel_alpha_i]
# save output
paras = np.array(paras)
np.save(paras_file, paras)
val_r2 = np.array(val_r2)
np.save(val_r2_file, val_r2)
alphas = np.array(alphas)
np.save(alphas_file, alphas)
def ridge_fitting(feat_dir, prf_dir, db_dir, subj_id, roi):
"""pRF model fitting using ridge regression.
90% trainning data used for model tuning, and another 10% data used for
model seletion.
"""
# load fmri response
vxl_idx, train_fmri_ts, val_fmri_ts = dataio.load_vim1_fmri(db_dir,
subj_id,
roi=roi)
del val_fmri_ts
print 'Voxel number: %s' % (len(vxl_idx))
# load candidate models
train_models = np.load(os.path.join(feat_dir, 'train_candidate_model.npy'),
mmap_mode='r')
# output directory config
roi_dir = os.path.join(prf_dir, roi)
check_path(roi_dir)
# model seletion and tuning
ALPHA_NUM = 20
BOOTS_NUM = 15
paras_file = os.path.join(roi_dir, 'reg_paras.npy')
paras = np.memmap(paras_file,
dtype='float64',
mode='w+',
shape=(42500, len(vxl_idx), 72))
mcorr_file = os.path.join(roi_dir, 'reg_model_corr.npy')
mcorr = np.memmap(mcorr_file,
dtype='float64',
mode='w+',
shape=(42500, len(vxl_idx)))
alphas_file = os.path.join(roi_dir, 'reg_alphas.npy')
alphas = np.memmap(alphas_file,
dtype='float64',
mode='w+',
shape=(42500, len(vxl_idx)))
# fMRI data z-score
print 'fmri data temporal z-score'
m = np.mean(train_fmri_ts, axis=1, keepdims=True)
s = np.std(train_fmri_ts, axis=1, keepdims=True)
train_fmri_ts = (train_fmri_ts - m) / (1e-10 + s)
# split training dataset into model tunning set and model selection set
tune_fmri_ts = train_fmri_ts[:, :int(1750 * 0.9)]
sel_fmri_ts = train_fmri_ts[:, int(1750 * 0.9):]
# model testing
for i in range(42500):
print 'Model %s' % (i)
# remove models which centered outside the 20 degree of visual angle
xi = (i % 2500) / 50
yi = (i % 2500) % 50
x0 = np.arange(5, 500, 10)[xi]
y0 = np.arange(5, 500, 10)[yi]
d = np.sqrt(np.square(x0 - 250) + np.square(y0 - 250))
if d > 249:
print 'Model center outside the visual angle'
paras[i, ...] = np.NaN
mcorr[i] = np.NaN
alphas[i] = np.NaN
continue
train_x = np.array(train_models[i, ...]).astype(np.float64)
train_x = zscore(train_x.T).T
# split training dataset into model tunning and selection sets
tune_x = train_x[:int(1750 * 0.9), :]
sel_x = train_x[int(1750 * 0.9):, :]
wt, r, alpha, bscores, valinds = ridge.bootstrap_ridge(
tune_x,
tune_fmri_ts.T,
sel_x,
sel_fmri_ts.T,
alphas=np.logspace(-2, 3, ALPHA_NUM),
nboots=BOOTS_NUM,
chunklen=175,
nchunks=1,
single_alpha=False,
use_corr=False)
paras[i, ...] = wt.T
mcorr[i] = r
alphas[i] = alpha
# save output
paras = np.array(paras)
np.save(paras_file, paras)
mcorr = np.array(mcorr)
np.save(mcorr_file, mcorr)
alphas = np.array(alphas)
np.save(alphas_file, alphas)