svgspnr - 10 months ago 74

Python Question

I have some netCDF files, 24 for each of the directions (

`x`

`y`

`z`

For the plotting I need to interpolate at specific point so I have to knew the nearest neighbor. My plan is to divide the data in to 3D cells so I don't have to search the nearest neighbor in the whole dataset.

So in my first step I read in my data files and create an array witch contains

`[x,y,z,v[:]]`

After that I calculate for each point the cell it belongs to and append it to a Array of 4 dimensions:

`x`

`y`

`z`

`v`

`for vec in vecs:`

x_ind = int((vec[0]-xmin) / stepWidthX)

y_ind = int((vec[1]-ymin) / stepWidthY)

z_ind = int((vec[2]-zmin) / stepWidthZ)

if x_ind==gridPointsInXdirection:

x_ind = x_ind-1

if y_ind==gridPointsInYdirection:

y_ind = y_ind-1

if z_ind==gridPointsInZdirection:

z_ind = z_ind-1

#print z_ind, y_ind,x_ind

XGridPoints[z_ind, y_ind, x_ind] = np.append(XGridPoints[z_ind, y_ind, x_ind], vec[0])

YGridPoints[z_ind, y_ind, x_ind] = np.append(YGridPoints[z_ind, y_ind, x_ind], vec[1])

ZGridPoints[z_ind, y_ind, x_ind] = np.append(ZGridPoints[z_ind, y_ind, x_ind], vec[2])

VGridPoints[z_ind, y_ind, x_ind] = np.append(VGridPoints[z_ind, y_ind, x_ind], vec[3])

Where

`vecs`

`VGridPoints`

`x = XGridPoints[2,3,4][2]`

y = YGridPoints[2,3,4][2]

z = ZGridPoints[2,3,4][2]

v[:] = VGridPoints[2,3,4][2]

When I take only one time step it's working but I have a large overdrive if I recalculate the cells and the nearest neighbour for each time step and they do not change the location over time.

Answer

Numpy is generally much more convenient if you know *a priori* the shape of the arrays you'll be working with. Things like appending to arrays suffer a performance penalty. I agree with Sebastian, that the easiest way (if possible) is to create an array large enough to hold everything (worst case scenario). If this is not possible then perhaps you can try with object arrays. For example, create an object array with the 3 spatial dimensions:

```
import numpy as N
XGridPoints = N.empty((nx, ny, nz), dtype='object')
```

(and the same for `YGridPoints`

, `ZGridPoints`

, `VGridPoints`

.) And then you can set `XGridPoints[z_ind, y_ind, x_ind]`

to a numpy array and append to that array as you need.