Python datasets.fetch_haxby函数代码示例

def test_fetch_haxby():
    for i in range(1, 6):
        haxby = datasets.fetch_haxby(data_dir=tmpdir, n_subjects=i,
                                     verbose=0)
        assert_equal(len(url_request.urls), 1 + (i == 1))  # subject_data + md5
        assert_equal(len(haxby.func), i)
        assert_equal(len(haxby.anat), i)
        assert_equal(len(haxby.session_target), i)
        assert_equal(len(haxby.mask_vt), i)
        assert_equal(len(haxby.mask_face), i)
        assert_equal(len(haxby.mask_house), i)
        assert_equal(len(haxby.mask_face_little), i)
        assert_equal(len(haxby.mask_house_little), i)
        url_request.reset()

def read_data_haxby(subject, tr=2.5, masker=False):
    haxby_dataset = fetch_haxby(subjects=[subject])

    # Load fmri data
    fmri_filename = haxby_dataset.func[0]
    fmri = load_img(fmri_filename)
    # mask = haxby_dataset.mask_vt[0]
    masker = NiftiMasker(mask_strategy='epi', standardize=True, detrend=True,
                         high_pass=0.01, t_r=tr, smoothing_fwhm=5)
    fmri = masker.fit_transform(fmri)
    fmri = fmri.reshape(12, -1, fmri.shape[-1])

    # Load stimuli data
    classes = np.array(['rest', 'face', 'house', 'bottle', 'cat', 'chair',
                        'scissors', 'shoe', 'scrambledpix'])
    labels = np.recfromcsv(
        haxby_dataset.session_target[0], delimiter=" ")['labels'].reshape(
            12, -1)
    stimuli, onsets, conditions = (np.zeros((
        12, len(labels[0]), len(classes))), [], [])
    stimuli[:, 0, 0] = 1
    for session in range(12):
        onsets.append([])
        conditions.append([])
        for scan in range(1, len(fmri[session])):
            if (labels[session][scan - 1] == 'rest' and
                labels[session][scan] != 'rest'):
                label = labels[session][scan]
                stimuli[session, scan, np.where(classes == label)[0][0]] = 1
                conditions[session].append(label)
                onsets[session].append(scan * tr)
            else:
                stimuli[session, scan, 0] = 1

    if subject == 5:
        fmri = np.vstack((fmri[:8], fmri[9:]))
        stimuli = np.vstack((stimuli[:8], stimuli[9:]))
        onsets = np.vstack((onsets[:8], onsets[9:]))
        conditions = np.vstack((conditions[:8], conditions[9:]))

    if masker:
        return fmri, stimuli, onsets, conditions, masker

    return fmri, stimuli, onsets, conditions

"""
NeuroImaging volumes visualization
==================================

Simple example to show Nifti data visualization.
"""

##############################################################################
# Fetch data
from nilearn import datasets

# By default 2nd subject will be fetched
haxby_dataset = datasets.fetch_haxby()

# print basic information on the dataset
print('First anatomical nifti image (3D) located is at: %s' %
      haxby_dataset.anat[0])
print('First functional nifti image (4D) is located at: %s' %
      haxby_dataset.func[0])

##############################################################################
# Visualization
from nilearn.image.image import mean_img

# Compute the mean EPI: we do the mean along the axis 3, which is time
func_filename = haxby_dataset.func[0]
mean_haxby = mean_img(func_filename)

from nilearn.plotting import plot_epi, show
plot_epi(mean_haxby)

----------
[1] Winkler, A. M. et al. (2014).
    Permutation inference for the general linear model. Neuroimage.

[2] Anderson, M. J. & Robinson, J. (2001).
    Permutation tests for linear models.
    Australian & New Zealand Journal of Statistics, 43(1), 75-88.
    (http://avesbiodiv.mncn.csic.es/estadistica/permut2.pdf)

"""
# Author: Virgile Fritsch, <[email protected]>, Feb. 2014

##############################################################################
# Load Haxby dataset
from nilearn import datasets
haxby_dataset = datasets.fetch_haxby(subjects=[2])

# print basic information on the dataset
print('Mask nifti image (3D) is located at: %s' % haxby_dataset.mask)
print('Functional nifti image (4D) is located at: %s' % haxby_dataset.func[0])

##############################################################################
# Mask data
mask_filename = haxby_dataset.mask
from nilearn.input_data import NiftiMasker
nifti_masker = NiftiMasker(
    smoothing_fwhm=8,
    mask_img=mask_filename,
    memory='nilearn_cache', memory_level=1)  # cache options
func_filename = haxby_dataset.func[0]
fmri_masked = nifti_masker.fit_transform(func_filename)

def _crop_mask(mask):
    """Crops input mask to produce tighter (i.e smaller) bounding box with
    the same support (active voxels)"""
    idx = np.where(mask)
    i_min = max(idx[0].min() - 1, 0)
    i_max = idx[0].max()
    j_min = max(idx[1].min() - 1, 0)
    j_max = idx[1].max()
    k_min = max(idx[2].min() - 1, 0)
    k_max = idx[2].max()
    return mask[i_min:i_max + 1, j_min:j_max + 1, k_min:k_max + 1]
    
### Load haxby dataset ########################################################
from nilearn.datasets import fetch_haxby
data_files = fetch_haxby('/home/eugene/Documents/')

### Load Target labels ########################################################
import numpy as np
labels = np.recfromcsv(data_files.session_target[0], delimiter=" ")


### split data into train and test samples ####################################
n_train=6
target = labels['labels']
condition_mask = np.logical_or(target == "scissors", target == "scrambledpix")
condition_mask_train = np.logical_and(condition_mask, labels['chunks'] <= n_train)
condition_mask_test = np.logical_and(condition_mask, labels['chunks'] > n_train)

# make X (design matrix) and y (response variable)
import nibabel

mask, and how simple operations can improve the quality of the mask
obtained.
"""
### Coordinates of the selected slice #########################################

coronal = -24
sagittal = -33
axial = -17
cut_coords = (coronal, sagittal, axial)

### Load the data #############################################################

# Fetch the data files from Internet
from nilearn import datasets
import nibabel
haxby_dataset = datasets.fetch_haxby(n_subjects=1)

# print basic information on the dataset
print('First subject anatomical nifti image (3D) located is at: %s' %
      haxby_dataset.anat[0])
print('First subject functional nifti image (4D) is located at: %s' %
      haxby_dataset.func[0])

# Second, load the labels
import numpy as np

session_target = np.recfromcsv(haxby_dataset.session_target[0], delimiter=" ")
haxby_labels = session_target['labels']

### Visualization function ####################################################

"""
Show stimuli of Haxby et al. dataset
===============================================================================

In this script we plot an overview of the stimuli used in "Distributed
and Overlapping Representations of Faces and Objects in Ventral Temporal
Cortex" (Science 2001)
"""

from scipy.misc import imread
import matplotlib.pyplot as plt

from nilearn import datasets

haxby_dataset = datasets.fetch_haxby(n_subjects=0, fetch_stimuli=True)
stimulus_information = haxby_dataset.stimuli

for stim_type in sorted(stimulus_information.keys()):
    if stim_type == "controls":
        # skip control images, there are too many
        continue

    file_names = stimulus_information[stim_type]

    plt.figure()
    for i in range(48):
        plt.subplot(6, 8, i + 1)
        try:
            plt.imshow(imread(file_names[i]), cmap=plt.cm.gray)
        except:
            # just go to the next one if the file is not present

"""
NeuroImaging volumes visualization
====================================

Simple example to show Nifti data visualization.
"""

### Fetch data ################################################################

from nilearn import datasets

haxby_files = datasets.fetch_haxby(n_subjects=1)

### Load an fMRI file #########################################################

import nibabel

fmri_img = nibabel.load(haxby_files.func[0])
fmri_data = fmri_img.get_data()
fmri_affine = fmri_img.get_affine()

### Visualization #############################################################

import numpy as np
import matplotlib.pyplot as plt

# Compute the mean EPI: we do the mean along the axis 3, which is time
mean_img = np.mean(fmri_data, axis=3)
# Note that this can also be done on Nifti images using
# nilearn.image.mean_img

"""
Decoding with SpaceNet: face vs house object recognition
=========================================================

Here is a simple example of decoding with a SpaceNet prior (i.e Graph-Net,
TV-l1, etc.), reproducing the Haxby 2001 study on a face vs house
discrimination task.

See also the SpaceNet documentation: :ref:`space_net`.
"""

##############################################################################
# Load the Haxby dataset
from nilearn.datasets import fetch_haxby

data_files = fetch_haxby()

# Load Target labels
import numpy as np

labels = np.recfromcsv(data_files.session_target[0], delimiter=" ")


# Restrict to face and house conditions
target = labels["labels"]
condition_mask = np.logical_or(target == b"face", target == b"house")

# Split data into train and test samples, using the chunks
condition_mask_train = np.logical_and(condition_mask, labels["chunks"] <= 6)
condition_mask_test = np.logical_and(condition_mask, labels["chunks"] > 6)

"""
Plot Haxby masks
=================

Small script to plot the masks of the Haxby dataset.
"""
from scipy import linalg
import matplotlib.pyplot as plt

from nilearn import datasets
data = datasets.fetch_haxby()

# Build the mean image because we have no anatomic data
from nilearn import image
mean_img = image.mean_img(data.func[0])

z_slice = -24
from nilearn.image.resampling import coord_transform
affine = mean_img.get_affine()
_, _, k_slice = coord_transform(0, 0, z_slice,
                                linalg.inv(affine))
k_slice = round(k_slice)

fig = plt.figure(figsize=(4, 5.4), facecolor='k')

from nilearn.plotting import plot_anat
display = plot_anat(mean_img, display_mode='z', cut_coords=[z_slice],
                    figure=fig)
display.add_contours(data.mask_vt[0], contours=1, antialiased=False,
                     linewidths=4., levels=[0], colors=['red'])
display.add_contours(data.mask_house[0], contours=1, antialiased=False,

This is a block-design fMRI dataset from a study on face and object\
 representation in human ventral temporal cortex. It consists of 6 subjects\
 with 12 runs per subject. In each run, the subjects passively viewed \
greyscale images of eight object categories, grouped in 24s blocks separated\
 by rest periods. Each image was shown for 500ms and was followed by a 1500ms\
 inter-stimulus interval. Full-brain fMRI data were recorded with a volume \
repetition time of 2.5s, thus, a stimulus block was covered by roughly 9 \
volumes.

Get full description <a href="http://dev.pymvpa.org/datadb/haxby2001.html">\
here</a>.\
"""

# fetch HAXBY dataset
N_SUBJECTS = 2
haxby_data = fetch_haxby(n_subjects=N_SUBJECTS)

# set output dir
OUTPUT_DIR = os.path.join(os.path.dirname(haxby_data.mask),
                          "haxby_runs")
if not os.path.exists(OUTPUT_DIR):
    os.makedirs(OUTPUT_DIR)

# get subject data
subjects = []
for subject_id in set([os.path.basename(os.path.dirname(x))
                       for x in haxby_data.func]):
    # instantiate subject_data object
    subject_data = SubjectData()
    subject_data.subject_id = subject_id
    subject_data.session_id = "haxby2001"

"""
Show stimuli of Haxby et al. dataset
===============================================================================

In this script we plot an overview of the stimuli used in "Distributed
and Overlapping Representations of Faces and Objects in Ventral Temporal
Cortex" (Science 2001)
"""

from scipy.misc import imread
import matplotlib.pyplot as plt

from nilearn import datasets
from nilearn.plotting import show

haxby_dataset = datasets.fetch_haxby(subjects=[], fetch_stimuli=True)
stimulus_information = haxby_dataset.stimuli

for stim_type in sorted(stimulus_information.keys()):
    if stim_type == b'controls':
        # skip control images, there are too many
        continue

    file_names = stimulus_information[stim_type]

    plt.figure()
    for i in range(48):
        plt.subplot(6, 8, i + 1)
        try:
            plt.imshow(imread(file_names[i]), cmap=plt.cm.gray)
        except:

from nilearn.datasets import fetch_haxby

haxby_data = fetch_haxby(n_subjects=1, fetch_stimuli=True)

"""
Show stimuli of Haxby et al. dataset
===============================================================================

In this script we plot an overview of the stimuli used in "Distributed
and Overlapping Representations of Faces and Objects in Ventral Temporal
Cortex" (Science 2001)
"""

from scipy.misc import imread
import matplotlib.pyplot as plt

from nilearn.datasets import fetch_haxby

stimulus_information = fetch_haxby(n_subjects=0,
                                   fetch_stimuli=True).stimuli

for stim_type in sorted(stimulus_information.keys()):
    if stim_type == "controls":
        # skip control images, there are too many
        continue

    file_names = stimulus_information[stim_type]

    plt.figure()
    for i in range(48):
        plt.subplot(6, 8, i + 1)
        try:
            plt.imshow(imread(file_names[i]))

            plt.gray()

    if axis is None:
        axis = 0
        array = array.ravel()

    array = np.rollaxis(array, axis)
    remaining_shape = array.shape[1:]
    length = len(array)

    array = array.reshape(length, -1)
    x = np.arange(length)
    x -= x.mean()
    x /= x.max()

    regressors = np.array([x ** order for order in range(polyorder + 1)]).T
    coef, resids, rank, s = lstsq(regressors, array)

    return coef.reshape([polyorder + 1] + list(remaining_shape))


if __name__ == "__main__":
    import nibabel as nb
    from nilearn.datasets import fetch_haxby
    h = fetch_haxby(n_subjects=1)
    data = nb.load(h.func[0]).get_data().T

    skewmap = skewness(data, axis=0)
    kurtmap = kurtosis(data, axis=0)
    trendmap = trend_coef(data, polyorder=2, axis=0)