Error about dimension about fit-sne

[dkobak]

Where exactly in test.ipynb do you get this error? The first time tsne is run? Please copy paste the terminal output.

[zhaixzh]

# Running t-SNE on the full MNIST in the default way (this uses perplexity=30) %time Z = fast_tsne(X50, seed=42) plt.figure(figsize=(5,5)) plt.scatter(Z[:,0], Z[:,1], c=col[y], s=.1) plt.tight_layout()

When I test this step，I encounter this error.
I use this test data and anthoer data，but after fast_tsne，the 'Z' is the same，should I add some parameters.
Thank you .

[dkobak]

Please post the terminal output here. Open the terminal window where you started the Python notebook and copy-paste the FIt-SNE output.

[zhaixzh]

`---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
~/.conda/envs/vev1/lib/python3.7/site-packages/matplotlib/axes/_axes.py in _parse_scatter_color_args(c, edgecolors, kwargs, xshape, yshape, get_next_color_func)
4290 valid_shape = False
-> 4291 raise ValueError
4292 except ValueError:

ValueError:

During handling of the above exception, another exception occurred:

ValueError Traceback (most recent call last)
in
4
5 plt.figure(figsize=(5,5))
----> 6 plt.scatter(Z[:,0], Z[:,1], c=col[y], s=.1)
7 plt.tight_layout()

~/.conda/envs/vev1/lib/python3.7/site-packages/matplotlib/pyplot.py in scatter(x, y, s, c, marker, cmap, norm, vmin, vmax, alpha, linewidths, verts, edgecolors, plotnonfinite, data, **kwargs)
2845 verts=verts, edgecolors=edgecolors,
2846 plotnonfinite=plotnonfinite, **({"data": data} if data is not
-> 2847 None else {}), **kwargs)
2848 sci(__ret)
2849 return __ret

~/.conda/envs/vev1/lib/python3.7/site-packages/matplotlib/init.py in inner(ax, data, *args, **kwargs)
1599 def inner(ax, *args, data=None, **kwargs):
1600 if data is None:
-> 1601 return func(ax, *map(sanitize_sequence, args), **kwargs)
1602
1603 bound = new_sig.bind(ax, *args, **kwargs)

~/.conda/envs/vev1/lib/python3.7/site-packages/matplotlib/axes/_axes.py in scatter(self, x, y, s, c, marker, cmap, norm, vmin, vmax, alpha, linewidths, verts, edgecolors, plotnonfinite, **kwargs)
4452 self._parse_scatter_color_args(
4453 c, edgecolors, kwargs, xshape, yshape,
-> 4454 get_next_color_func=self._get_patches_for_fill.get_next_color)
4455
4456 if plotnonfinite and colors is None:

~/.conda/envs/vev1/lib/python3.7/site-packages/matplotlib/axes/_axes.py in _parse_scatter_color_args(c, edgecolors, kwargs, xshape, yshape, get_next_color_func)
4296 "acceptable for use with 'x' with size {xs}, "
4297 "'y' with size {ys}."
-> 4298 .format(nc=n_elem, xs=xsize, ys=ysize)
4299 )
4300 else:

ValueError: 'c' argument has 70000 elements, which is not acceptable for use with 'x' with size 25000, 'y' with size 25000.`

[dkobak]

No, sorry, that's not what I meant. I need to see the FIt-SNE output. It should look like this:

=============== t-SNE v1.1.0 ===============
fast_tsne data_path: data.dat
fast_tsne result_path: result.dat
fast_tsne nthreads: 8
Read the following parameters:
...

and quite a lot afterwards.

What you copied are Python errors when running plt.scatter. What I need, is Python output when running fast_tsne.

[zhaixzh]

I have solved the problem. I changed the terminal, then normal running, it should be configuration problem. Thank you .