Illustration and main functionalities and inputs of the cross-section object. .. image:: ../../picture/picobjects/ex_cs_obj.png """ from visbrain.objects import CrossSecObj, SceneObj from visbrain.io import download_file sc = SceneObj() print(""" # ============================================================================= # Brodmann area # ============================================================================= """) cs_brod = CrossSecObj('brodmann', interpolation='nearest', section=(70, 80, 90)) cs_brod.localize_source((-10., -15., 20.)) sc.add_to_subplot(cs_brod, row=0, col=0, title='Brodmann area') print(""" # ============================================================================= # Nii.gz file # ============================================================================= """) path = download_file('GG-853-GM-0.7mm.nii.gz') cs_cust = CrossSecObj(path, section=(90, 80, 100), cmap='gist_stern') sc.add_to_subplot(cs_cust, row=0, col=1, title='Nii.gz file') sc.preview()
from visbrain.objects import VolumeObj, CrossSecObj, SourceObj from visbrain.io import download_file """Download two NIFTI files """ path_1 = download_file('GG-853-GM-0.7mm.nii.gz', astype='example_data') path_2 = download_file('GG-853-WM-0.7mm.nii.gz', astype='example_data') """Define four sources sources and a Source object """ s_xyz = np.array([[29.9, -37.3, -19.3], [-5.33, 14.00, 20.00], [25.99, 14.00, 34.66], [0., -1.99, 10.66]]) s_obj = SourceObj('MySources', s_xyz) """Define a volume object and a cross-section object """ vol_obj = VolumeObj(path_1) cross_sec_obj = CrossSecObj(path_2) """Localize a source in the cross-section object """ cross_sec_obj.localize_source(s_xyz[2, :]) """Define a Brain instance and pass the source, volume and cross-section object """ vb = Brain(source_obj=s_obj, vol_obj=vol_obj, cross_sec_obj=cross_sec_obj) vb.show()
pic_height=21., cmap='viridis') sc.add_to_subplot(pic_obj, row=1, col=2, title='3D pictures') sc.add_to_subplot(BrainObj('B2'), use_this_cam=True, row=1, col=2) ############################################################################### # Connectivity ############################################################################### arch = np.load(download_file('phase_sync_delta.npz', astype='example_data')) nodes, edges = arch['nodes'], arch['edges'] c_count = ConnectObj('default', nodes, edges, select=edges > .7, color_by='count', antialias=True, line_width=2., dynamic=(.1, 1.)) s_obj_c = SourceObj('sources', nodes, color='#ab4642', radius_min=5.) sc.add_to_subplot(c_count, row=2, col=0, row_span=2, title='3D connectivity') sc.add_to_subplot(s_obj_c, row=2, col=0) sc.add_to_subplot(BrainObj('B3'), use_this_cam=True, row=2, col=0) ############################################################################### # Cross-sections ############################################################################### cs_brod = CrossSecObj('brodmann', interpolation='nearest', coords=(70, 80, 90), cmap='viridis') cs_brod.localize_source((-10., -15., 20.)) sc.add_to_subplot(cs_brod, row=2, col=1, col_span=2, row_span=2, title='Cross-sections') sc.preview()
from visbrain.objects import VolumeObj, CrossSecObj, SourceObj from visbrain.io import download_file """Download two NIFTI files """ path_1 = download_file('GG-853-GM-0.7mm.nii.gz') path_2 = download_file('GG-853-WM-0.7mm.nii.gz') """Define four sources sources and a Source object """ s_xyz = np.array([[29.9, -37.3, -19.3], [-5.33, 14.00, 20.00], [25.99, 14.00, 34.66], [0., -1.99, 10.66]]) s_obj = SourceObj('MySources', s_xyz) """Define a volume object and a cross-section object """ vol_obj = VolumeObj(path_1) cross_sec_obj = CrossSecObj(path_2) """Localize a source in the cross-section object """ cross_sec_obj.localize_source(s_xyz[2, :]) """Define a Brain instance and pass the source, volume and cross-section object """ vb = Brain(source_obj=s_obj, vol_obj=vol_obj, cross_sec_obj=cross_sec_obj) vb.show()