Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[BUG] SINDyDerivative does not handle PDEs #472

Open
yb6599 opened this issue Feb 7, 2024 · 2 comments · May be fixed by #476
Open

[BUG] SINDyDerivative does not handle PDEs #472

yb6599 opened this issue Feb 7, 2024 · 2 comments · May be fixed by #476
Labels
bug Something isn't working

Comments

@yb6599
Copy link
Contributor

yb6599 commented Feb 7, 2024

I am trying to differentiate pde data of shape (256, 100, 1) and len(t_train)=100 and I keep getting an error with the message "Invalid shape of X". Here is the simplified version of the code and the corresponding error.

Reproducing code example:

import numpy as np
import pysindy as ps

X = np.random.random(size=(256, 100, 1))
t = np.arange(0, 10, 0.1)
differentiator = ps.SINDyDerivative(kind='kalman')
differentiator._differentiate(X, t)

Error message:

{
	"name": "ValueError",
	"message": "Invalid shape of X.",
	"stack": "---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
File d:\\UW\\Research\\gen-experiments\\src\\gen_experiments\\debug.py:30
     28 t = np.arange(0, 10, 0.1)
     29 differentiator = ps.SINDyDerivative(kind='kalman')
---> 30 differentiator._differentiate(X, t)

File d:\\UW\\Research\\gen-experiments\\env\\Lib\\site-packages\\pysindy\\differentiation\\sindy_derivative.py:79, in SINDyDerivative._differentiate(self, x, t)
     74     t = arange(x.shape[0]) * t
     76 differentiator = methods[self.kwargs[\"kind\"]](
     77     **{k: v for k, v in self.kwargs.items() if k != \"kind\"}
     78 )
---> 79 x_dot = differentiator.d(x, t, axis=0)
     80 if self.save_smooth:
     81     self.smoothed_x_ = differentiator.x(x, t, axis=0)

File d:\\UW\\Research\\gen-experiments\\env\\Lib\\site-packages\\derivative\\differentiation.py:194, in Derivative.d(self, X, t, axis)
    176 def d(self, X, t, axis=1):
    177     \"\"\"
    178     Compute the derivative of measurements X taken at times t.
    179 
   (...)
    192         ValueError: Requires that X.shape[axis] equals len(t). If X is flat, requires that len(X) equals len(t).
    193     \"\"\"
--> 194     X, flat = _align_axes(X, t, axis)
    196     if X.shape[1] == 1:
    197         dX = X

File d:\\UW\\Research\\gen-experiments\\env\\Lib\\site-packages\\derivative\\differentiation.py:245, in _align_axes(X, t, axis)
    243         raise ValueError(\"Invalid axis.\")
    244 else:
--> 245     raise ValueError(\"Invalid shape of X.\")
    247 if X.shape[1] != len(t):
    248     raise ValueError(\"Desired X axis size does not match t size.\")

ValueError: Invalid shape of X."
}

PySINDy/Python version information:

1.7.6.dev215+g9c73768 3.11.7 (tags/v3.11.7:fa7a6f2, Dec 4 2023, 19:24:49) [MSC v.1937 64 bit (AMD64)]

@Jacob-Stevens-Haas Jacob-Stevens-Haas changed the title [BUG] Error in derivative package when differentiating data [BUG] SINDyDerivative does not handle PDEs Feb 7, 2024
@Jacob-Stevens-Haas
Copy link
Collaborator

Jacob-Stevens-Haas commented Feb 7, 2024

I think this is because BaseDifferentiation subclasses don't all handle the axis kwarg correctly, e.g.

ps.SINDyDerivative(kind="kalman")(X, t, axis=1)
# TypeError: __init__() got an unexpected keyword argument 'axis'

ps.FiniteDifference()(X, t)
# Error, expected, because no way that FiniteDifference knows to differentiate the second axis

ps.SpectralDerivative()(X, t)
# no error, but should, because Spectral is assuming it should differentiate the 0th axis

ps.FiniteDifference(axis=1)(X, t)
# no error, correct

ps.SmoothedFiniteDifference(axis=1)(X, t)
# correct, behaves like FiniteDifference

@yb6599
Copy link
Contributor Author

yb6599 commented May 9, 2024

This is not an issue on pysindy version 1.7.6.dev278+g098d231, but is an issue on pysindy version 1.7.6.dev315+ga43e217

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

Successfully merging a pull request may close this issue.

2 participants