I'm relatively new to all this and I started the tutorial on image analysis here. When trying to perform the pylab.imshow(dna)
step it returns the following error:
In [10]: pylab.imshow(dna)
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-10-fc86cadb4e46> in <module>()
----> 1 pylab.imshow(dna)
/usr/lib/pymodules/python2.7/matplotlib/pyplot.pyc in imshow(X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, shape, filternorm, filterrad, imlim, resample, url, hold, **kwargs)
2375 ax.hold(hold)
2376 try:
-> 2377 ret = ax.imshow(X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, shape, filternorm, filterrad, imlim, resample, url, **kwargs)
2378 draw_if_interactive()
2379 finally:
/usr/lib/pymodules/python2.7/matplotlib/axes.pyc in imshow(self, X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, shape, filternorm, filterrad, imlim, resample, url, **kwargs)
6794 filterrad=filterrad, resample=resample, **kwargs)
6795
-> 6796 im.set_data(X)
6797 im.set_alpha(alpha)
6798 self._set_artist_props(im)
/usr/lib/pymodules/python2.7/matplotlib/image.pyc in set_data(self, A)
409 if (self._A.ndim not in (2, 3) or
410 (self._A.ndim == 3 and self._A.shape[-1] not in (3, 4))):
--> 411 raise TypeError("Invalid dimensions for image data")
412
413 self._imcache =None
TypeError: Invalid dimensions for image data
Fairly certain I have followed all the instructions in the tutorial to the letter but I can't work out was is going wrong.
it's just what the image is saved as in dna = mahotas.imread('dna.jpeg') type(dna) gives numpy.ndarray and dna.shape gives (1024, 1344, 1)
This is the problem, if you pass a 3D ndarray
, it expects that you will have 3 or 4 planes (RGB or RGBA) (Read the code on line 410 in the last frame of the stack trace).
You just need to get rid of the extra dimension using
dna = dna.squeeze()
or
imshow(dna.squeeze())
To see what squeeze
is doing, see the following example:
a = np.arange(25).reshape(5, 5, 1)
print a.shape # (5, 5, 1)
b = a.squeeze()
print b.shape # (5, 5)
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