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', )