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")
