not finding POT

[Estudiant-roqueta]

I have POT, pymanopt autograd following POT instructions in https://pythonot.github.io/index.html. I made git clone of this github to try the tutorials and so. everything installed, most of them work. But when I try to run Tuto-GUDHI-Barycenters-of-persistence.diagrams.ipyb when it calls bary this happens:

b, log = bary(diags,
init=0,
verbose=True) # we initialize our estimation on the first diagram (the red one.)

NameError Traceback (most recent call last)
~\AppData\Local\Temp/ipykernel_10868/2194333359.py in
----> 1 b, log = bary(diags,
2 init=0,
3 verbose=True) # we initialize our estimation on the first diagram (the red one.)

~\anaconda3\lib\site-packages\gudhi\wasserstein\barycenter.py in lagrangian_barycenter(pdiagset, init, verbose)
92 # the points of Y.
93 # If points disappear, there thrown
---> 94 # on [0,0] by default.
95 new_created_points = [] # will store potential new points.
96

~\anaconda3\lib\site-packages\gudhi\wasserstein\wasserstein.py in wasserstein_distance(X, Y, matching, order, internal_p, enable_autodiff, keep_essential_parts)
319 if matching:
320 assert not enable_autodiff, "matching and enable_autodiff are currently incompatible"
--> 321 P = ot.emd(a=a,b=b,M=M, numItermax=2000000)
322 ot_cost = np.sum(np.multiply(P,M))
323 P[-1, -1] = 0 # Remove matching corresponding to the diagonal

NameError: name 'ot' is not defined

I revised the files and they import OT correctly. I even tried to put "import ot" in the exact subprocess but even then it does not recognize it.

[VincentRouvreau]

@Estudiant-roqueta As you have conda, here is the list of commands that works for me:

conda create -n tda-tutorial
conda activate tda-tutorial
conda install -c conda-forge python
which python  # check it is somewhere in .../envs/tda-tutorial/...
pip install -r .binder/requirements.txt
pip install jupyter
jupyter notebook

And from here, barycenter notebook works fine for me (with gudhi 3.5.0).

It seems to you have a python kernel in your notebook that is not the one with which you installed pot or something like that.
If you import ot in a notebook cell, do you have any error ?
And what if you do import gudhi.wasserstein in a notebook cell ?

[bghattas]

I have a similar error when calling the barry function

b, log = bary(diags,
init=0,
verbose=True) # we initialize our estimation on the first diagram (the red one.)
in the Tuto-GUDHI-Barycenters-of-persistence-diagrams notebook.

I am running the notebook through google collab, i have installed the pot module and "import ot" executes without warning..
Nevertheless, i have the following error

NameError Traceback (most recent call last)
in <cell line: 1>()
----> 1 b, log = bary(diags,
2 init=0,
3 verbose=True) # we initialize our estimation on the first diagram (the red one.)

1 frames
/usr/local/lib/python3.10/dist-packages/gudhi/wasserstein/wasserstein.py in wasserstein_distance(X, Y, matching, order, internal_p, enable_autodiff, keep_essential_parts)
319 if matching:
320 assert not enable_autodiff, "matching and enable_autodiff are currently incompatible"
--> 321 P = ot.emd(a=a,b=b,M=M, numItermax=2000000)
322 ot_cost = np.sum(np.multiply(P,M))
323 P[-1, -1] = 0 # Remove matching corresponding to the diagonal

NameError: name 'ot' is not defined

[mglisse]

I just tried on google colab, I added a code cell with !pip install POT gudhi at the beginning of the notebook, and it ran just fine...

[bghattas]

thank you @mglisse, i had only to reinitialise my session for that to work !