godfreap - 7 months ago 43

Python Question

This is relating to my last question, which can be found here. I'm dealing with lists similar to the list I describe in that link as markerList - so a list with three levels. I need to save this information as a .mat file, but I can't get it to save in the right type. When using scipy.io.savemat, it saves the list as a 200x40x2 single, when it should be a set of 200 cells, each containing a 40x2 cell.

The code I'm using to save this is:

`matdict = dict(markers = (markerList), sorted = (finalStack))`

scipy.io.savemat('C:\pathname\\sortedMarkers.mat', matdict)

What is confusing to me is that it saves markerList in the correct format (1x200 cell, each a cell of varying size), but not finalStack (saved as a 200 x 40 x 2 single). On top of that, before I had figured out the rest of this code, it would save finalStack correctly - which makes me think that perhaps it saves as a cell when the data it is saving isn't uniform in size. (finalStack is uniform in size; markerList is not.)

Is there a way to save a complicated data structure like this as a .mat file?

Answer

As per savemat documentation, convert into a numpy array of 'objects':

```
from scipy.io import savemat
import numpy
a = numpy.array([[1,2,3],[1,2,3]])
b = numpy.array([[2,3,4],[2,3,4]])
c = numpy.array([[3,4,5],[3,4,5]])
L = [a,b,c]
FrameStack = numpy.empty((len(L),), dtype=numpy.object)
for i in range(len(L)):
FrameStack[i] = L[i]
savemat("myfile.mat", {"FrameStack":FrameStack})
```

In octave:

```
>> load myfile.mat
>> whos FrameStack
Variables in the current scope:
Attr Name Size Bytes Class
==== ==== ==== ===== =====
FrameStack 1x3 144 cell
Total is 3 elements using 144 bytes
>> whos FrameStack{1}
Variables in the current scope:
Attr Name Size Bytes Class
==== ==== ==== ===== =====
FrameStack{1} 2x3 48 int64
Total is 6 elements using 48 bytes
```