Plotting 3D surface in Python with dataframe

Question

I am fairly new to Python, so I sorry if my question is not as coherent as a fluent python user, but I have searched the web and really haven't found a solution for what I am trying to do. I have a set of experimental data in a csv file that I would like to plot as a 3D surface. It is structured as follows:

               x(time)
y(depth)   z(temperature readings)
y          z(temperature readings)
y          z(temperature readings)
y          z(temperature readings)

Basically, my top row and my left hand column should function as x,y parts of a depth time array and the z is the temperature reading at each x,y coordinate.

I have tried setting my x and y as arrays and then using meshgrid(x,y) to set up a grid. But my z is values, not an explicit function of x,y. So I can't get it to work. I tried referencing the z using x,y but that didn't seem to work.

I have also tried importing it as a dataframe and playing around with 3D plotting options, but they all seem to require a format of:

   x y z
   .....
   .....
   .....

which doesn't help with my dataset. I would appreciate any ideas/suggestions on this! Thanks.

s-m-e · Accepted Answer · 2017-05-06 12:46:11Z

1

How about this for a start? The data reading and re-shaping part is not the fastest and most reliable on the planet - you might use some battle-proven Pandas routines instead if you do this sort of work on a larger scale - but the example might give you an insight into how this can be done.

from plotly.offline import plot
from plotly.graph_objs import Figure, Layout, Surface

# Some "random" data in the desired format
some_data = """depth;1;2;3;4
0.2;0;1;1;0
0.4;0.2;1.4;1.6;0.8
0.6;0.3;1.2;1.7;0.7
0.8;0.1;0.8;1.1;0.3
"""

# Iterate over lines in data - bringing it into shape
data_z = []
data_y = []
for line_index, line in enumerate(some_data.split('\n')):
    # Get time vector (x)
    if line_index == 0:
        data_x = [float(x) for x in line.split(';')[1:]]
    # Get z-values
    else:
        # If line is not empty
        if line != '':
            data_z.append([float(z) for z in line.split(';')[1:]])
            data_y.append(float(line.split(';')[0]))

# Prepare a plot
fig = Figure(
    data = [
        Surface(
            x = data_x,
            y = data_y,
            z = data_z
        )
    ],
    layout = Layout(
        title = 'some data plot',
        autosize = True
        )
    )

# Spit it out ...
plot(fig, filename='some-data-surface')

answered May 6, 2017 at 12:46

s-m-e

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1 Comment

bwindi Over a year ago

Thanks. That is enough to get me started. I thought pandas would have something more obvious but I certainly haven't found it. I'll give this a shot and see how I do. Thanks again.

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