I solved the issue by creating a matrix with all the unique x and y values filling this with the corresponding z value and then filling the empty spaces with NaN. This way I am able to use the contourf for plotting.
from example
2000 2500 3000
20 rand NaN rand
30 NaN rand NaN
40 rand NaN NaN
50 NaN rand NaN
60 rand NaN rand
70 NaN rand NaN
