python pandas dataframe to matlab struct using scipy.io

Question

I am trying to save a pandas dataframe to a matlab .mat file using scipy.io.

I have the following:

array1 = np.array([1,2,3])
array2 = np.array(['a','b','c'])
array3 = np.array([1.01,2.02,3.03])
df = DataFrame({1:array1, 2:array2,3:array3}, index=('array1','array2','array3'))
recarray_ = df.to_records()
## Produces:
# rec.array([('array1', 1, 'a', 1.01), ('array2', 2, 'b', 2.02),
#   ('array3', 3, 'c', 3.03)], 
#  dtype=[('index', 'O'), ('1', '<i4'), ('2', 'O'), ('3', '<f8')])
scipy.io.savemat('test_recarray_struct.mat', {'struct':df.to_records()})

In Matlab, I would expect this to produce a struct containing three arrays (one int, one char, one float) but it actually produces is a struct containing 3 more structs, each containing four variables; 'index', 1, '2', 3. When trying to select 1, '2' or 3 I get the error 'The variable struct(1, 1).# does not exist.'

Can anyone explain the expected behaviour and how best to save DataFrames to .mat files?

mat4mlw · Accepted Answer · 2015-06-08 10:49:59Z

4

I am using the following workaround in the meantime. Please let me know if you have a better solution:

a_dict = {col_name : df[col_name].values for col_name in df.columns.values}

## optional if you want to save the index as an array as well:
# a_dict[df.index.name] = df.index.values
scipy.io.savemat('test_struct_to_mat.mat', {'struct':a_dict})

edited Jun 8, 2015 at 10:49

answered Jun 8, 2015 at 10:42

mat4mlw

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Comments

Nenad Propadović · Accepted Answer · 2017-12-05 12:58:24Z

1

I think what you need is to create the dataframe like this:

df = DataFrame({'array1':array1, 'array2':array2,'array3':array3})

and save it like this:

scipy.io.savemat('test_recarray_struct.mat', {'struct':df.to_dict("list")})

So the code should be something like:

# ... import appropritely
array1 = np.array([1,2,3])
array2 = np.array(['a','b','c'])
array3 = np.array([1.01,2.02,3.03])
df = DataFrame({'array1':array1, 'array2':array2,'array3':array3})
scipy.io.savemat('test_recarray_struct.mat', {'struct':df.to_dict("list")})

edited Dec 5, 2017 at 12:58

answered Dec 5, 2017 at 12:50

Nenad Propadović

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1 Comment

Nenad Propadović Over a year ago

Hello pashute, I checked what I wrote (on two computers) and it worked for me. Is there something about the solution that doesn't work for you? Cheers, Nenad

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