def test_contours_substitutions():
import itertools
import matplotlib.pyplot as plt
from samri.plotting.maps import contour_slices
from samri.utilities import bids_substitution_iterator
subjects = [
'4007',
]
contrasts = [
#'bold',
'cbv',
]
for i in list(itertools.product(subjects, contrasts)):
file_template = '{{data_dir}}/preprocessing/sub-{{subject}}/ses-{{session}}/func/sub-{{subject}}_ses-{{session}}_task-JogB_acq-EPIlowcov_run-{{run}}_{}.nii.gz'.format(
i[1])
substitutions = bids_substitution_iterator(
sessions=[
'ofM',
'ofMaF',
'ofMcF1',
'ofMcF2',
],
subjects=[i[0]],
runs=[0, 1],
data_dir='/usr/share/samri_bidsdata',
validate_for_template=file_template,
)
cmap = plt.get_cmap('tab20').colors
contour_slices(
'/usr/share/mouse-brain-atlases/dsurqec_40micron.nii',
alpha=[0.6],
colors=cmap[::2],
figure_title='Multi-Session Fit and Coherence Control',
file_template=file_template,
force_reverse_slice_order=True,
legend_template='{session} session',
levels_percentile=[77],
save_as='_contours_multi_{}_{}.pdf'.format(i[0], i[1]),
slice_spacing=0.45,
substitutions=substitutions,
)
def test_contours_substitutions():
import itertools
import matplotlib.pyplot as plt
from samri.plotting.maps import contour_slices
from samri.utilities import bids_substitution_iterator
subjects = [
'4007',
]
contrasts= [
#'bold',
'cbv',
]
for i in list(itertools.product(subjects, contrasts)):
file_template='{{data_dir}}/preprocessing/sub-{{subject}}/ses-{{session}}/func/sub-{{subject}}_ses-{{session}}_task-JogB_acq-EPIlowcov_run-{{run}}_{}.nii.gz'.format(i[1])
substitutions = bids_substitution_iterator(
sessions=[
'ofM',
'ofMaF',
'ofMcF1',
'ofMcF2',
],
subjects=[i[0]],
runs=[0,1],
data_dir='/usr/share/samri_bidsdata',
validate_for_template=file_template,
)
cmap = plt.get_cmap('tab20').colors
contour_slices('/usr/share/mouse-brain-atlases/dsurqec_40micron.nii',
alpha=[0.6],
colors=cmap[::2],
figure_title='Multi-Session Fit and Coherence Control',
file_template=file_template,
force_reverse_slice_order=True,
legend_template='{session} session',
levels_percentile=[77],
save_as='_contours_multi_{}_{}.pdf'.format(i[0],i[1]),
slice_spacing=0.45,
substitutions=substitutions,
)
def test_contours_single():
from samri.plotting.maps import contour_slices
import matplotlib.pyplot as plt
file_template = '/usr/share/mouse-brain-atlases/dsurqec_200micron_masked.nii'
cmap = plt.get_cmap('tab20').colors
contour_slices('/usr/share/samri_bidsdata/preprocessing/sub-4007/ses-ofM/func/sub-4007_ses-ofM_task-JogB_acq-EPIlowcov_run-1_cbv.nii.gz',
alpha=[0.9],
colors=cmap[::2],
figure_title='Single-Session Fit and Distortion Control',
file_template=file_template,
force_reverse_slice_order=True,
legend_template='Template',
levels_percentile=[79],
ratio=[7,5],
slice_spacing=0.45,
save_as='_contours_single.pdf',
)
def test_contours_single():
from samri.plotting.maps import contour_slices
import matplotlib.pyplot as plt
file_template = '/usr/share/mouse-brain-atlases/dsurqec_200micron_masked.nii'
cmap = plt.get_cmap('tab20').colors
contour_slices(
'/usr/share/samri_bidsdata/preprocessing/sub-4007/ses-ofM/func/sub-4007_ses-ofM_task-JogB_acq-EPIlowcov_run-1_cbv.nii.gz',
alpha=[0.9],
colors=cmap[::2],
figure_title='Single-Session Fit and Distortion Control',
file_template=file_template,
force_reverse_slice_order=True,
legend_template='Template',
levels_percentile=[79],
ratio=[7, 5],
slice_spacing=0.45,
save_as='_contours_single.pdf',
)