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Black background when plotting brains in PDF #870

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AlexandreAbraham opened this issue Dec 2, 2015 · 15 comments
Open

Black background when plotting brains in PDF #870

AlexandreAbraham opened this issue Dec 2, 2015 · 15 comments
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Plotting The issue is related to plotting functionalities.

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@AlexandreAbraham
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Steps to reproduce:

  • Run this script:
from nilearn.plotting import plot_stat_map
import numpy as np
import nibabel
import pylab as pl


a = nibabel.Nifti1Image(np.zeros((10, 10, 10)), np.eye(4))
plot_stat_map(a)
pl.savefig('test.pdf')
  • Open test.pdf using Inkscape.
  • Save it as test_.pdf
  • Open test_.pdf in evince: the background appears black.
@lesteve
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lesteve commented Dec 2, 2015

Just checking the original test.pdf is fine, right?

@AlexandreAbraham
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That depends. If you try to print it, it should be black. I just provided a
way to reproduce it using inkscape not to print one sheet of paper
everytime we want to test a solution.

Alex.

On Wed, Dec 2, 2015 at 3:02 PM, Loïc Estève notifications@github.com
wrote:

Just checking the original test.pdf is fine, right?

—
Reply to this email directly or view it on GitHub
#870 (comment).

@GaelVaroquaux
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GaelVaroquaux commented Dec 2, 2015 via email

@lesteve
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lesteve commented Dec 2, 2015

OK that makes slightly more sense now, thanks.

@AlexandreAbraham
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This patch solves the problem: https://github.com/matplotlib/matplotlib/pull/4595/files

It is hardly backportable.

@GaelVaroquaux
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GaelVaroquaux commented Dec 2, 2015 via email

@lesteve
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lesteve commented Dec 2, 2015

At least it looks like the fix is in matplotlib 1.5.0: https://github.com/matplotlib/matplotlib/blob/v1.5.0/lib/matplotlib/tests/test_backend_pdf.py#L126.

@AlexandreAbraham
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Yes, the bug is solved in 1.5

@lesteve
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lesteve commented Dec 2, 2015

Maybe we should close this one, since we are not planning to do anything about it.

@AlexandreAbraham
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I am actually trying to solve it right now.

@GaelVaroquaux
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GaelVaroquaux commented Dec 2, 2015 via email

@AlexandreAbraham
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For the record, I tried to backport the PDF backend from matplotlib 1.5.0 into 1.4.3 but there are too many modifications. So I tried to apply the patch mentioned above and, for some reason, it doesn't work.

I'm a bit helpless :-/ on this one.

@thomasbazeille
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not sure whether this issue persists. No one complained for a while, will check when i have time

@jeromedockes
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tried it now, I can reproduce the issue

@Remi-Gau Remi-Gau added the Plotting The issue is related to plotting functionalities. label Mar 21, 2023
@Remi-Gau
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Remi-Gau commented Sep 3, 2024

Can reproduce

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@GaelVaroquaux @AlexandreAbraham @lesteve @thomasbazeille @Remi-Gau @jeromedockes