def setUp(self): ''' load inital parameters and/or data for testing''' self.fnameAdj = 'data/3d_grid_adj.txt' self.fnameCo = 'data/3d_grid_coords.txt' self.fnameProps = 'data/3d_grid_properties.txt' # initialise brain and plot objects self.a = mb.brainObj() self.b = plotObj() # some data self.edges = [(0,2),(0,4),(0,6)] self.locations = {0:(1,1,1), 2:(2,2,2), 4:(3,3,3), 6:(4,4,4)}
def setUp(self): ''' load inital parameters and/or data for testing''' self.fnameAdj = 'data/3d_grid_adj.txt' self.fnameCo = 'data/3d_grid_coords.txt' self.fnameProps = 'data/3d_grid_properties.txt' # initialise brain and plot objects self.a = mb.brainObj() self.b = plotObj() # some data self.edges = [(0, 2), (0, 4), (0, 6)] self.locations = { 0: (1, 1, 1), 2: (2, 2, 2), 4: (3, 3, 3), 6: (4, 4, 4) }
a.localThresholding(edgePC=edgePC) #weights = [weightDict[e]+1.0 for e in a.G.edges()] #weights = [power(v,4)*v for v in weights] # fudge the sizes a bit so there is more of a contrast, ie take the square sizeList = [power(degs[v],2) for v in a.G.nodes()] # import the spatial file a.importSpatialInfo(spatFile) # import MNI space as a background brain a.importBackground("/usr/share/data/fsl-mni152-templates/MNI152_T1_2mm_brain.nii.gz") # create a plotting object b = mbp.plotObj() # plot the brain edges b.plotBrainEdges(a, opacity=0.7, lw=3.) #, scalars=weights #plot the brain nodes b.plotBrainCoords(a, col=(0.,0.,1.), sizeList = sizeList, opacity=0.5, sf=4.) # plot the background MNI space b.plotSkull(a, contourVals = [3000,9000]) #fEnd = "edgesOnly" fEnd = None saveFig(a, d, outDir, fEnd=fEnd, fType=".png")