Exemplo n.º 1
0
    def readXYZ(self):
        
        # Create coordinate space based on x,y,z dimensions, and multiply by affine matrix
        # Examples shown if xdim = 3, ydim=4, zdim=5
        # Create R row variable [1 2 3 1 2 3...] ydim * zdim times
        Rrow = list(scinu.seq(1,self.xdim)) * (self.ydim*self.zdim)

        # Create C row variable [1 1 1 2 2 2 3 3 3 4 4 4 1 1 1 2 2 2...] zdim X
        Crow = []
        for y in range(1,self.ydim+1):
            for x in range(0,self.xdim):
                Crow.append(y)
        Crow = Crow * self.zdim
	
        # Create P row variable [ each of 1:zdim xdim*ydim times ]
        Prow = []
        for z in range(1,self.zdim+1):
            holder = ([z] * self.xdim*self.ydim)
            for i in holder:
                Prow.append(i)

        # Create row of 1s of length zdim*xdim*ydim so we can multiply matrices
        onedim = [1] * self.xdim * self.ydim * self.zdim

        # Stack each row on top of one another
        self.RCP = np.vstack((Rrow,Crow,Prow,onedim))

        # Make it into a matrix
        self.RCP = scinu.mat(self.RCP)

        # Grab the first three rows of the affine transformation matrix (4th is for time)
        affXYZ = self.aff[0:3]

        # Multiply affine transformation matrix by coordinate data to go from coordinate --> MNI space
        self.XYZ = affXYZ * self.RCP
Exemplo n.º 2
0
    def readXYZ(self):
        # I couldn't get this method to work, but will keep to try again...
        # R, C, P = scinu.ndgrid(scinu.seq(1,3),scinu.seq(1,4),scinu.seq(1,5))

        # Create coordinate space based on x,y,z dimensions, and multiply by affine matrix
        # Examples shown if xdim = 3, ydim=4, zdim=5
        # Create R row variable [1 2 3 1 2 3...] ydim * zdim times
        Rrow = list(scinu.seq(1, self.xdim)) * (self.ydim * self.zdim)

        # Create C row variable [1 1 1 2 2 2 3 3 3 4 4 4 1 1 1 2 2 2...] zdim X
        Crow = []
        for y in range(1, self.ydim + 1):
            for x in range(0, self.xdim):
                Crow.append(y)
        Crow = Crow * self.zdim

        # Create P row variable [ each of 1:zdim xdim*ydim times ]
        Prow = []
        for z in range(1, self.zdim + 1):
            holder = ([z] * self.xdim * self.ydim)
            for i in holder:
                Prow.append(i)

# Create row of 1s of length zdim*xdim*ydim so we can multiply matrices
        onedim = [1] * self.xdim * self.ydim * self.zdim

        # Stack each row on top of one another
        self.RCP = np.vstack((Rrow, Crow, Prow, onedim))

        # Make it into a matrix
        self.RCP = scinu.mat(self.RCP)

        # Grab the first three rows of the affine transformation matrix (4th is for time)
        affXYZ = self.aff[0:3]

        # Multiply affine transformation matrix by coordinate data to go from coordinate --> MNI space
        self.XYZ = affXYZ * self.RCP
Exemplo n.º 3
0
 def readAff(self):
     self.aff = scinu.mat(self.img.get_affine())
Exemplo n.º 4
0
 def readAff(self):
     self.aff = scinu.mat(self.img.get_affine())