def test_show_design_matrix():
# test that the show code indeed (formally) runs
frame_times = np.linspace(0, 127 * 1., 128)
dmtx = make_first_level_design_matrix(frame_times,
drift_model='polynomial',
drift_order=3)
ax = plot_design_matrix(dmtx)
assert (ax is not None)
with InTemporaryDirectory():
ax = plot_design_matrix(dmtx, output_file='dmtx.png')
assert os.path.exists('dmtx.png')
assert (ax is None)
plot_design_matrix(dmtx, output_file='dmtx.pdf')
assert os.path.exists('dmtx.pdf')
def _dmtx_to_svg_url(design_matrices):
"""Accepts a FirstLevelModel or SecondLevelModel object
with fitted design matrices & generates SVG Image URL,
which can be inserted into an HTML template.
Parameters
----------
design_matrices : List[pd.Dataframe]
Design matrices computed in the model.
Returns
-------
svg_url_design_matrices : String
SVG Image URL for the plotted design matrices.
"""
html_design_matrices = []
dmtx_template_path = os.path.join(HTML_TEMPLATE_ROOT_PATH,
'design_matrix_template.html'
)
with open(dmtx_template_path) as html_template_obj:
dmtx_template_text = html_template_obj.read()
for dmtx_count, design_matrix in enumerate(design_matrices, start=1):
dmtx_text_ = string.Template(dmtx_template_text)
dmtx_plot = plot_design_matrix(design_matrix)
dmtx_title = 'Session {}'.format(dmtx_count)
plt.title(dmtx_title, y=0.987)
dmtx_plot = _resize_plot_inches(dmtx_plot, height_change=.3)
url_design_matrix_svg = _plot_to_svg(dmtx_plot)
# prevents sphinx-gallery & jupyter from scraping & inserting plots
plt.close()
dmtx_text_ = dmtx_text_.safe_substitute(
{'design_matrix': url_design_matrix_svg,
'dmtx_title': dmtx_title,
}
)
html_design_matrices.append(dmtx_text_)
svg_url_design_matrices = ''.join(html_design_matrices)
return svg_url_design_matrices
# preprocess the data
subject_data = do_subjects_preproc(jobfile, dataset_dir=dataset_dir)[0]
# construct design matrix
nscans = len(subject_data.func[0])
frametimes = np.linspace(0, (nscans - 1) * tr, nscans)
drift_model = 'Cosine'
hrf_model = 'spm + derivative'
design_matrix = make_first_level_design_matrix(frametimes,
paradigm,
hrf_model=hrf_model,
drift_model=drift_model,
high_pass=hfcut)
# plot and save design matrix
ax = plot_design_matrix(design_matrix)
ax.set_position([.05, .25, .9, .65])
ax.set_title('Design matrix')
dmat_outfile = os.path.join(subject_data.output_dir, 'design_matrix.png')
plt.savefig(dmat_outfile, bbox_inches="tight", dpi=200)
# specify contrasts
contrasts = {}
_, matrix, names = check_design_matrix(design_matrix)
contrast_matrix = np.eye(len(names))
for i in range(len(names)):
contrasts[names[i]] = contrast_matrix[i]
# more interesting contrasts"""
contrasts = {'active-rest': contrasts['active'] - contrasts['rest']}
