Bug when using the function "iterative_prewhitening"

[stefano-rgc]

After I made a fresh installation of the IvSPythonRepository and the corresponding Conda environment, I get a Python TypeError when running the following code:

>>>from ivs.timeseries.freqanalyse import iterative_prewhitening
>>>from ivs.timeseries.freqanalyse import stopcrit_scargle_snr
>>>import numpy as np
>>>
>>>t = np.arange(100)
>>>s = np.sin(t)
>>>
>>>iterative_prewhitening(t, s)
Frequency precision not reached with stepsize 6.464646e-08 , breaking loop
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/lhome/stefano/Python/packages/ivs/timeseries/freqanalyse.py", line 379, in iterative_prewhitening
    prewhiteningorder_snr_window=prewhiteningorder_snr_window,**kwargs)
  File "/lhome/stefano/Python/packages/ivs/timeseries/freqanalyse.py", line 326, in find_frequency
    params = numpy_ext.recarr_join(params,errors)
  File "/lhome/stefano/Python/packages/ivs/aux/numpy_ext.py", line 374, in recarr_join
    arr1 = append_fields(arr1,field,arr2[field],asrecarray=False)
  File "/lhome/stefano/anaconda3/envs/ivs_repo_3.6/lib/python3.6/site-packages/numpy/lib/recfunctions.py", line 651, in append_fields
    base = merge_arrays(base, usemask=usemask, fill_value=fill_value)
  File "/lhome/stefano/anaconda3/envs/ivs_repo_3.6/lib/python3.6/site-packages/numpy/lib/recfunctions.py", line 382, in merge_arrays
    seqarrays = seqarrays.ravel()
  File "/lhome/stefano/anaconda3/envs/ivs_repo_3.6/lib/python3.6/site-packages/numpy/ma/core.py", line 4517, in ravel
    r = ndarray.ravel(self._data, order=order).view(type(self))
TypeError: descriptor 'ravel' requires a 'numpy.ndarray' object but received a 'numpy.void'

Timothy identified the problem in the function recarr_join within the file ivs/aux/numpy_ext.py.

In the version I am using, such function reads (note the commented line):

def recarr_join(arr1,arr2):
    """
    Join to record arrays column wise.
    """
    arr1 = arr1.copy()
    for field in arr2.dtype.names:
        # arr1 = pl.mlab.rec_append_fields(arr1,field,arr2[field])
        arr1 = append_fields(arr1,field,arr2[field],asrecarray=False)
    return arr1

While in the working version of Timothy, the same function reads:

def recarr_join(arr1,arr2):
    """
    Join to record arrays column wise.
    """
    arr1 = arr1.copy()
    for field in arr2.dtype.names:
        arr1 = pl.mlab.rec_append_fields(arr1,field,arr2[field])
    return arr1

I have now changed my local version of the IvS repository but I think the change should be done in the official version too.

[karandis]

Hi Stefano,

Thanks for bringing this up. I double-checked, and I had commented out that line because the function rec_append_fields() is depreciated and has been removed in matplotlib 3.1.

https://matplotlib.org/3.0.0/api/mlab_api.html#matplotlib.mlab.rec_append_fields

I will try to look for an alternative :)

Cheers, Karan

[LucIJspeert]

Hi Karan,

I have had trouble with this functionality as well: the problem is that recarrays have been moved from mpl to numpy, but it's only in numpy 1.15 and up (which is a higher version than the repository environment has).

The functionality can now be found under: np.lib.recfunctions.rec_append_fields() https://numpy.org/devdocs/user/basics.rec.html - (search for 'rec_append_fields')

As a side note, depending on the functionality you need, structured arrays might be a good alternative.

Cheers, Luc

[karandis]

Hi Luc,

Awesome! have you tested this function on your local repository? If it works in the way that it's intended to, then I'll update the version of numpy and implement it :)

Cheers, Karan

[LucIJspeert]

Yeah it works, I use that in my local version of the repository, along with al the updated packages. :) In fact, you can find the change here in my fork: https://github.com/LucIJspeert/IvSPythonRepository/commit/abec847ea13be5f94be8daa385a34d3b5dbab210

[karandis]

Hi everyone, I have updated the repository to reflect the changes. Could you please check if it works now @stefano-rgc?

Cheers, Karan