diff options
Diffstat (limited to 'nitime/fmri')
-rw-r--r-- | nitime/fmri/hrf.py | 2 | ||||
-rw-r--r-- | nitime/fmri/io.py | 4 | ||||
-rw-r--r-- | nitime/fmri/tests/test_io.py | 5 |
3 files changed, 6 insertions, 5 deletions
diff --git a/nitime/fmri/hrf.py b/nitime/fmri/hrf.py index 61123da..82f9269 100644 --- a/nitime/fmri/hrf.py +++ b/nitime/fmri/hrf.py @@ -1,6 +1,6 @@ from __future__ import print_function import numpy as np -from scipy.misc import factorial +from scipy.special import factorial def gamma_hrf(duration, A=1., tau=1.08, n=3, delta=2.05, Fs=1.0): diff --git a/nitime/fmri/io.py b/nitime/fmri/io.py index 55d4e6f..e54f86b 100644 --- a/nitime/fmri/io.py +++ b/nitime/fmri/io.py @@ -88,7 +88,7 @@ def time_series_from_file(nifti_files, coords=None, TR=None, normalize=None, if verbose: print("Reading %s" % nifti_files) im = load(nifti_files) - data = im.get_data() + data = im.get_fdata() # If coordinates are provided as input, read data only from these coordinates: if coords is not None: #If the input is the coords of several ROIs @@ -118,7 +118,7 @@ def time_series_from_file(nifti_files, coords=None, TR=None, normalize=None, if verbose: print("Reading %s" % f) im = load(f) - data = im.get_data() + data = im.get_fdata() if coords is not None: #If the input is the coords of several ROIs if isinstance(coords, tuple) or isinstance(coords, list): diff --git a/nitime/fmri/tests/test_io.py b/nitime/fmri/tests/test_io.py index 973e599..8a5d78e 100644 --- a/nitime/fmri/tests/test_io.py +++ b/nitime/fmri/tests/test_io.py @@ -7,6 +7,7 @@ import os import numpy as np import numpy.testing as npt +import pytest import nitime import nitime.timeseries as ts @@ -22,7 +23,7 @@ except ImportError as e: data_path = os.path.join(nitime.__path__[0],'data') -@npt.dec.skipif(no_nibabel,no_nibabel_msg) +@pytest.mark.skipif(no_nibabel, reason=no_nibabel_msg) def test_time_series_from_file(): """Testing reading of data from nifti files, using nibabel""" @@ -64,7 +65,7 @@ def test_time_series_from_file(): npt.assert_equal(t4.sampling_interval,nitime.TimeArray(1.35)) # Test the default behavior: - data = io.load(fmri_file1).get_data() + data = io.load(fmri_file1).get_fdata() t5 = ts_ff(fmri_file1) npt.assert_equal(t5.shape, data.shape) npt.assert_equal(t5.sampling_interval, ts.TimeArray(1, time_unit='s')) |