Scale bar does not correspond to the actual size

[Alexandre de Siqueira]

Dear all,
first of all, thank you very much for this, scalebars are kinda mandatory in research and having this in python is really nice.
I am having some issues when using ScaleBar. The bar does not correspond to the actual size it would have; could you help me with that?
I'm using this code:

from matplotlib_scalebar.scalebar import ScaleBar
from skimage.io import imread

len_px = 0.00048223304582578836

image = imread('dur_grain1apatite01.tif', as_grey=True)

fig, ax = plt.subplots(figsize=(15, 10))
ax.imshow(testimg_apatite)
scalebar = ScaleBar(dx=len_px,
                    units='mm',
                    fixed_value=25,
                    fixed_units='um',
                    location=4,
                    box_alpha=0,
                    font_properties={'family' : 'monospace',
                                     'weight' : 'semibold',
                                     'size' : 20})
fig.gca().add_artist(scalebar)
plt.show()

This is the example image.
Thank you very much for your support.

[parishcm]

I've noticed the same behavior, using ImageJ to measure the scalebar and "set scale", followed by measuring the full width of the image with ctrl-M in ImageJ. The code below makes a 100 pix image with 0.1 micron/pixel, for 10 microns in extent. If we use the default length_fraction the scale bar is 1 micron and the image is about 9.3 microns measured. With length_fraction = 0.7, the scale bar is 5 microns and the extent (measured in ImageJ) is perfect.

Anyway -- thanks for this! It's awesome. I'm writing a script to dump CrossCourt4 data as a batch export and this will help a lot.

import numpy as np
import matplotlib.pyplot as plt
from matplotlib_scalebar.scalebar import ScaleBar

A = 2 * np.random.rand(110, 100) - 1
A[100:110, :] = np.nan

f, c = plt.subplots()
cax = plt.imshow(A, cmap='bwr')
f.colorbar(cax)
cax.axes.get_xaxis().set_visible(False)
cax.axes.get_yaxis().set_visible(False)
plt.axis('off')

dx = 0.1

scale = ScaleBar(dx, 'um', location='lower left', length_fraction = 0.7)
plt.gca().add_artist(scale)

[Philippe Pinard]

Thank you both for your comment. You are 100% right there was a mistake in the code. After many attempts to understand the problem I realized that the "bar" of the scale bar was drawn with an edge around it 😞 This made the "bar" appeared longer. Making the bar longer (with the length_fraction) helped because the error due to the edge decreases as the length of the bar increases.

I tried @parishcm's example and I got a length of 10.0769 in ImageJ. I committed a fix and I will release a new version soon.

[Firas Moosvi]

I just noticed this issue also because I tried to make the bar thicker but the size of the bar changed so I got suspicious. Any update on a fix, would be great to get an ETA so I can wait it out or try to apply the commit myself (could you ref the commit here?)

[Firas Moosvi]

Oops! Sorry just noticed it's commit 7f3683a and v5. Will update and check back

[Philippe Pinard]

I will close this issue not to cause confusion. Please reopen if you think the problem is still there.